Test cutadapt 3.5+galaxy1 #22

jennaj · 2022-02-24T00:07:22Z

Reported issues with "submit" button not actually submitting -- can reproduce at org, ran fine when originally installed ref galaxyproject/usegalaxy-playbook#347

tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1

jennaj · 2022-02-24T00:07:46Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1

mvdbeek · 2022-02-24T00:12:21Z

Results (powered by Planemo)

Summary

State	Count
Total	33
Passed	23
Error	0
Failure	10
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ebi_search_rest_results 0.1.1 #14)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test Prokka 1.14.6+galaxy1 #3)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test cutadapt 3.5+galaxy1 #22)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test rseqc_bam2wig 2.6.4 #23)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test gops_coverage_1 1.0.0 #24)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test spades 3.12.0+galaxy1 and 3.15.3+galaxy2 #25)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test test ncbi_datasets #29)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ggplot2_point 3.3.5+galaxy0 #30)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test trinotate 3.2.2+galaxy0 #6)
Problems:
- 'command_line'

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test pangolin 3.1.17+galaxy1 #7)

Problems:

Output json_stats:  different than expected, difference (using diff):
( /tmp/tmp57hd3mrrcutadapt_rest.json v. /tmp/tmpfclqgxyacutadapt_rest.json )
--- local_file
+++ history_data
@@ -4,7 +4,7 @@
   "cutadapt_version": "3.5",
   "python_version": "3.9.7",
   "command_line_arguments": [
-    "-j=1",
+    "-j=6",
     "--json",
     "stats.json",
     "-a",
@@ -17,7 +17,7 @@
     "--action=trim",
     "cutadapt_rest_fa.fa"
   ],
-  "cores": 1,
+  "cores": 6,
   "input": {
     "path1": "cutadapt_rest_fa.fa",
     "path2": null,

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 --json stats.json -a AAAGATG --rest-file=rest_output.fa --output=out1.fa --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_rest_fa.fa
Processing reads on 6 cores in single-end mode ...
Finished in 0.06 s (11350 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       5
Reads with adapters:                         5 (100.0%)
Reads written (passing filters):             5 (100.0%)

Total basepairs processed:            97 bp
Total written (filtered):             35 bp (36.1%)

=== Adapter 1 ===

Sequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times

Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
7	1	0.0	0	1
12	1	0.0	0	1
14	2	0.0	0	2
15	1	0.0	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696660, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAGATG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`["rest_file", "json_stats"]`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

Passed s

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test tool test #1)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.06 s (21291 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696665, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test test against test.galaxyproject.org #2)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz
Processing reads on 6 cores in single-end mode ...
Finished in 0.07 s (672 µs/read; 0.09 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         2 (2.0%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Total written (filtered):         24,843 bp (100.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696666, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test racon 1.3.1.1 #11)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -g file:/corral4/main/objects/f/3/c/dataset_f3cd3a63-3166-455d-ad9e-69a80274fd46.dat --output=split/{name}.fastq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq_gz.fq.gz
Processing reads on 6 cores in single-end mode ...
Finished in 0.08 s (7263 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                      11
Reads with adapters:                        10 (90.9%)
Reads written (passing filters):            11 (100.0%)

Total basepairs processed:         1,210 bp
Total written (filtered):          1,130 bp (93.4%)

=== Adapter A2 ===

Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5


=== Adapter A1 ===

Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696663, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 93696664, "src": "hda"}]}, "front_adapter_source_list": "file"}, "single_noindels": "false"}]}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"multiple_output"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test mafft 7.221.3 #12)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AAAT --untrimmed-output=untrimmed_output.fq --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.06 s (19593 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)

== Read fate breakdown ==
Reads discarded as untrimmed:                2 (66.7%)
Reads written (passing filters):             1 (33.3%)

Total basepairs processed:           102 bp
Total written (filtered):             30 bp (29.4%)

=== Adapter 1 ===

Sequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-4 bp: 0

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
4	1	0.0	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696695, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"untrimmed_file"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ebi_metagenomics_run_downloader 0.1.0 #13)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGATCGGAAGAGC --untrimmed-output=untrimmed_output.fq.gz --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz
Processing reads on 6 cores in single-end mode ...
Finished in 0.07 s (721 µs/read; 0.08 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         2 (2.0%)

== Read fate breakdown ==
Reads discarded as untrimmed:               97 (98.0%)
Reads written (passing filters):             2 (2.0%)

Total basepairs processed:        24,849 bp
Total written (filtered):            496 bp (2.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696691, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"untrimmed_file"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test tp_sort_rows 1.0.0 #15)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (17668 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             87 bp (85.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696705, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test tp_sorted_uniq 1.0.0 #16)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --rename={id} barcode={cut_prefix} cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (15228 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             87 bp (85.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696705, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": "{id} barcode={cut_prefix}", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test hyphy_gard 2.5.31+galaxy1 #17)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=retain cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (17478 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             80 bp (78.4%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696703, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "retain", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test prokka 1.14.6+galaxy1 #18)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=mask cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (16460 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696705, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "mask", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test build_ucsc_custom_track_1 1.0.0 (+ 1.0.1 once updated on org) #19)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=lowercase cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.09 s (29851 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696705, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "lowercase", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test roary 3.13.0+galaxy2 #20)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=none cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (16722 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696705, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "none", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test mothur_align_seqs 1.39.5.0 #21)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a TAAACAGATTAGT --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --revcomp cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (17143 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reverse-complemented:                        0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             97 bp (95.1%)

=== Adapter 1 ===

Sequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 100.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
5	1	0.0	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696705, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "TAAACAGATTAGT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "true", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test circos 0.69.8+galaxy7 #26)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.06 s (19389 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             20 bp (19.6%)

=== Adapter 1 ===

Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696731, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "3prime", "shorten_values": "True"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test macs2_callpeak 2.1.1.20160309.6 #27)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.06 s (18832 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             20 bp (19.6%)

=== Adapter 1 ===

Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696731, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "5prime", "shorten_values": "True"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test table_annovar 0.2 #28)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGCGGCTTAGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --max-expected-errors=10 cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.07 s (22630 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)

== Read fate breakdown ==
Reads with too many exp. errors:             0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696731, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCGGCTTAGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "10", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test roary 3.13.0+galaxy2 #4)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/corral4/main/jobs/040/959/40959799/outputs/galaxy_dataset_79586acf-a10b-457f-b6c7-10e13f519ee7.dat --paired-output=/corral4/main/jobs/040/959/40959799/outputs/galaxy_dataset_3134684e-2b40-4a39-9208-b7f5c92cd0b6.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz
Processing reads on 6 cores in paired-end mode ...
Finished in 0.08 s (783 µs/read; 0.08 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       4 (4.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Total written (filtered):         49,677 bp (100.0%)
  Read 1:        24,843 bp
  Read 2:        24,834 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 50.0%
  T: 50.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2
4	1	0.4	0	1
5	1	0.1	0	1

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 2, "input_1": {"values": [{"id": 1398719, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test circos 0.69.8+galaxy10 #32)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --output=/corral4/main/jobs/040/959/40959860/outputs/galaxy_dataset_7aee8adf-2631-4311-9d04-34729fdb7887.dat --paired-output=/corral4/main/jobs/040/959/40959860/outputs/galaxy_dataset_e0085730-5528-4881-b0e0-bc93a1ab7c3b.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz
Processing reads on 6 cores in paired-end mode ...
Finished in 0.20 s (1983 µs/read; 0.03 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       4 (4.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Total written (filtered):         49,677 bp (100.0%)
  Read 1:        24,843 bp
  Read 2:        24,834 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 50.0%
  T: 50.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2
4	1	0.4	0	1
5	1	0.1	0	1

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 2, "input_1": {"values": [{"id": 1398721, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "true"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "true"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test strelka #33)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/corral4/main/jobs/040/959/40959861/outputs/galaxy_dataset_d7c43c85-7607-4f4f-888c-b986b7b7234f.dat --paired-output=/corral4/main/jobs/040/959/40959861/outputs/galaxy_dataset_68b6460f-6fde-4cb1-8652-76f95ecc4e6b.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any --quality-cutoff=5 Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz -Q=15,20
Processing reads on 6 cores in paired-end mode ...
Finished in 0.09 s (959 µs/read; 0.06 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       2 (2.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Quality-trimmed:                     747 bp (1.5%)
  Read 1:             0 bp
  Read 2:           747 bp
Total written (filtered):         48,938 bp (98.5%)
  Read 1:        24,843 bp
  Read 2:        24,095 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	1.5	0	1
4	1	0.4	0	1

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 2, "input_1": {"values": [{"id": 1398723, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": "15,20"}, "type": "paired_collection"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "5", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 bwa-mem-fastq1_fq_gz.fq.gz
Processing reads on 6 cores in single-end mode ...
Finished in 0.09 s (863 µs/read; 0.07 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         4 (4.0%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     286 bp (1.2%)
Total written (filtered):         24,550 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 75.0%
  G: 25.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	3	1.5	0	3
4	1	0.4	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696666, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "20", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test gffread 2.2.1.3+galaxy0 #9)

Command Line:

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93696665, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`["report", "info_file"]`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test trim_galore 0.6.7+galaxy0 #10)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.7
Command line parameters: -j=6 -g A1=^GTCGGTAA -g A2=^AGGTCACT --output=split/{name}.fastq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.10 s (9472 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                      11
Reads with adapters:                        10 (90.9%)
Reads written (passing filters):            11 (100.0%)

Total basepairs processed:         1,210 bp
Total written (filtered):          1,130 bp (93.4%)

=== Adapter A1 ===

Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5


=== Adapter A2 ===

Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 0, "input_1": {"values": [{"id": 93696657, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^GTCGGTAA", "front_adapter_name": "A1", "front_adapter_source_list": "user"}, "single_noindels": "false"}, {"__index__": 1, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^AGGTCACT", "front_adapter_name": "A2", "front_adapter_source_list": "user"}, "single_noindels": "false"}]}, "type": "single"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"multiple_output"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

jennaj · 2022-02-25T23:22:38Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1

mvdbeek · 2022-02-25T23:27:02Z

Results (powered by Planemo)

Summary

State	Count
Total	33
Passed	23
Error	0
Failure	10
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ebi_search_rest_results 0.1.1 #14)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test Prokka 1.14.6+galaxy1 #3)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test cutadapt 3.5+galaxy1 #22)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test rseqc_bam2wig 2.6.4 #23)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test gops_coverage_1 1.0.0 #24)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test spades 3.12.0+galaxy1 and 3.15.3+galaxy2 #25)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test test ncbi_datasets #29)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ggplot2_point 3.3.5+galaxy0 #30)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test trinotate 3.2.2+galaxy0 #6)
Problems:
- 'command_line'

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test pangolin 3.1.17+galaxy1 #7)

Problems:

Output json_stats:  different than expected, difference (using diff):
( /tmp/tmpzhfgubalcutadapt_rest.json v. /tmp/tmpdr6yfasecutadapt_rest.json )
--- local_file
+++ history_data
@@ -2,9 +2,9 @@
   "tag": "Cutadapt report",
   "schema_version": [0, 1],
   "cutadapt_version": "3.5",
-  "python_version": "3.9.7",
+  "python_version": "3.9.10",
   "command_line_arguments": [
-    "-j=1",
+    "-j=6",
     "--json",
     "stats.json",
     "-a",
@@ -17,7 +17,7 @@
     "--action=trim",
     "cutadapt_rest_fa.fa"
   ],
-  "cores": 1,
+  "cores": 6,
   "input": {
     "path1": "cutadapt_rest_fa.fa",
     "path2": null,

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 --json stats.json -a AAAGATG --rest-file=rest_output.fa --output=out1.fa --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_rest_fa.fa
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (10324 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                       5
Reads with adapters:                         5 (100.0%)
Reads written (passing filters):             5 (100.0%)

Total basepairs processed:            97 bp
Total written (filtered):             35 bp (36.1%)

=== Adapter 1 ===

Sequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times

Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
7	1	0.0	0	1
12	1	0.0	0	1
14	2	0.0	0	2
15	1	0.0	0	1

Job Parameters:

Job parameter	Parameter value
output_selector	`["rest_file", "json_stats"]`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798354, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAGATG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

Passed s

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test tool test #1)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (18268 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798353, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test test against test.galaxyproject.org #2)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz
Processing reads on 6 cores in single-end mode ...
Finished in 0.07 s (679 µs/read; 0.09 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         2 (2.0%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Total written (filtered):         24,843 bp (100.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798355, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test racon 1.3.1.1 #11)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -g file:/corral4/main/objects/1/1/6/dataset_1162d192-be38-448e-afff-ea509a979f1d.dat --output=split/{name}.fastq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq_gz.fq.gz
Processing reads on 6 cores in single-end mode ...
Finished in 0.11 s (10444 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                      11
Reads with adapters:                        10 (90.9%)
Reads written (passing filters):            11 (100.0%)

Total basepairs processed:         1,210 bp
Total written (filtered):          1,130 bp (93.4%)

=== Adapter A2 ===

Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5


=== Adapter A1 ===

Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798351, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 93798358, "src": "hda"}]}, "front_adapter_source_list": "file"}, "single_noindels": "false"}]}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"multiple_output"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test mafft 7.221.3 #12)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AAAT --untrimmed-output=untrimmed_output.fq --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.06 s (21184 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)

== Read fate breakdown ==
Reads discarded as untrimmed:                2 (66.7%)
Reads written (passing filters):             1 (33.3%)

Total basepairs processed:           102 bp
Total written (filtered):             30 bp (29.4%)

=== Adapter 1 ===

Sequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-4 bp: 0

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
4	1	0.0	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798403, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"untrimmed_file"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ebi_metagenomics_run_downloader 0.1.0 #13)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC --untrimmed-output=untrimmed_output.fq.gz --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz
Processing reads on 6 cores in single-end mode ...
Finished in 0.11 s (1142 µs/read; 0.05 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         2 (2.0%)

== Read fate breakdown ==
Reads discarded as untrimmed:               97 (98.0%)
Reads written (passing filters):             2 (2.0%)

Total basepairs processed:        24,849 bp
Total written (filtered):            496 bp (2.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798394, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"untrimmed_file"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test tp_sort_rows 1.0.0 #15)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.04 s (14081 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             87 bp (85.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798403, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test tp_sorted_uniq 1.0.0 #16)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --rename={id} barcode={cut_prefix} cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.04 s (14255 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             87 bp (85.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798411, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": "{id} barcode={cut_prefix}", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test hyphy_gard 2.5.31+galaxy1 #17)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=retain cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (17341 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             80 bp (78.4%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798413, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "retain", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test prokka 1.14.6+galaxy1 #18)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=mask cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.07 s (23772 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798434, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "mask", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test build_ucsc_custom_track_1 1.0.0 (+ 1.0.1 once updated on org) #19)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=lowercase cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (17680 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798413, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "lowercase", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test roary 3.13.0+galaxy2 #20)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=none cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (15764 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798413, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "none", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test mothur_align_seqs 1.39.5.0 #21)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a TAAACAGATTAGT --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --revcomp cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (17168 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reverse-complemented:                        0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             97 bp (95.1%)

=== Adapter 1 ===

Sequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 100.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
5	1	0.0	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798413, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "TAAACAGATTAGT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "true", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test circos 0.69.8+galaxy7 #26)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (16695 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             20 bp (19.6%)

=== Adapter 1 ===

Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798442, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "3prime", "shorten_values": "True"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test macs2_callpeak 2.1.1.20160309.6 #27)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.07 s (23863 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             20 bp (19.6%)

=== Adapter 1 ===

Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798442, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "5prime", "shorten_values": "True"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test table_annovar 0.2 #28)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGCGGCTTAGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --max-expected-errors=10 cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.08 s (25910 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)

== Read fate breakdown ==
Reads with too many exp. errors:             0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798442, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCGGCTTAGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "10", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test roary 3.13.0+galaxy2 #4)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/corral4/main/jobs/041/013/41013886/outputs/galaxy_dataset_d8231fe5-11dd-4b48-a0f7-aafb60b18082.dat --paired-output=/corral4/main/jobs/041/013/41013886/outputs/galaxy_dataset_03530eb9-0254-4fb3-8367-d54c6afc1ff4.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz
Processing reads on 6 cores in paired-end mode ...
Finished in 0.05 s (538 µs/read; 0.11 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       4 (4.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Total written (filtered):         49,677 bp (100.0%)
  Read 1:        24,843 bp
  Read 2:        24,834 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 50.0%
  T: 50.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2
4	1	0.4	0	1
5	1	0.1	0	1

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 2, "input_1": {"values": [{"id": 1403309, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test circos 0.69.8+galaxy10 #32)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --output=/corral4/main/jobs/041/013/41013948/outputs/galaxy_dataset_6cb2afbc-609a-45cc-81ac-4a45534f0d53.dat --paired-output=/corral4/main/jobs/041/013/41013948/outputs/galaxy_dataset_f5174832-8554-4668-b988-2413513930f9.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz
Processing reads on 6 cores in paired-end mode ...
Finished in 0.06 s (603 µs/read; 0.10 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       4 (4.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Total written (filtered):         49,677 bp (100.0%)
  Read 1:        24,843 bp
  Read 2:        24,834 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 50.0%
  T: 50.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2
4	1	0.4	0	1
5	1	0.1	0	1

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 2, "input_1": {"values": [{"id": 1403312, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "true"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "true"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test strelka #33)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/corral4/main/jobs/041/013/41013949/outputs/galaxy_dataset_2e5e3289-248e-4524-9a57-5f66d35ce01b.dat --paired-output=/corral4/main/jobs/041/013/41013949/outputs/galaxy_dataset_b1498efd-e30f-4f42-88a7-1c83ce7e2a6d.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any --quality-cutoff=5 Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz -Q=15,20
Processing reads on 6 cores in paired-end mode ...
Finished in 0.05 s (514 µs/read; 0.12 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       2 (2.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Quality-trimmed:                     747 bp (1.5%)
  Read 1:             0 bp
  Read 2:           747 bp
Total written (filtered):         48,938 bp (98.5%)
  Read 1:        24,843 bp
  Read 2:        24,095 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	1.5	0	1
4	1	0.4	0	1

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 2, "input_1": {"values": [{"id": 1403314, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": "15,20"}, "type": "paired_collection"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "5", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 bwa-mem-fastq1_fq_gz.fq.gz
Processing reads on 6 cores in single-end mode ...
Finished in 0.07 s (718 µs/read; 0.08 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         4 (4.0%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     286 bp (1.2%)
Total written (filtered):         24,550 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 75.0%
  G: 25.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	3	1.5	0	3
4	1	0.4	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798355, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "20", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test gffread 2.2.1.3+galaxy0 #9)

Command Line:

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 93798353, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`["report", "info_file"]`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test trim_galore 0.6.7+galaxy0 #10)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -g A1=^GTCGGTAA -g A2=^AGGTCACT --output=split/{name}.fastq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (4284 µs/read; 0.01 M reads/minute).

=== Summary ===

Total reads processed:                      11
Reads with adapters:                        10 (90.9%)
Reads written (passing filters):            11 (100.0%)

Total basepairs processed:         1,210 bp
Total written (filtered):          1,130 bp (93.4%)

=== Adapter A1 ===

Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5


=== Adapter A2 ===

Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 0, "input_1": {"values": [{"id": 93798349, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^GTCGGTAA", "front_adapter_name": "A1", "front_adapter_source_list": "user"}, "single_noindels": "false"}, {"__index__": 1, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^AGGTCACT", "front_adapter_name": "A2", "front_adapter_source_list": "user"}, "single_noindels": "false"}]}, "type": "single"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"multiple_output"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

jennaj · 2022-03-08T22:32:16Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1

mvdbeek · 2022-03-09T01:43:45Z

Results (powered by Planemo)

Summary

State	Count
Total	33
Passed	19
Error	0
Failure	14
Skipped	0

Failed s

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test test against test.galaxyproject.org #2)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Command Line:

Exit Code:

```
255
```

Standard Error:

FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94223960, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ebi_search_rest_results 0.1.1 #14)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test Prokka 1.14.6+galaxy1 #3)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test cutadapt 3.5+galaxy1 #22)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test rseqc_bam2wig 2.6.4 #23)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test gops_coverage_1 1.0.0 #24)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test spades 3.12.0+galaxy1 and 3.15.3+galaxy2 #25)
Problems:
- 'command_line'

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test macs2_callpeak 2.1.1.20160309.6 #27)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Command Line:

Exit Code:

```
255
```

Standard Error:

FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94226578, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "5prime", "shorten_values": "True"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test test ncbi_datasets #29)
Problems:
- 'command_line'
❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ggplot2_point 3.3.5+galaxy0 #30)
Problems:
- 'command_line'

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test roary 3.13.0+galaxy2 #4)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Collection element forward of collection out_pairs:  different than expected, difference (using diff):
( /tmp/tmpu6ejby3ocutadapt_out1.fq.gz v. /tmp/tmpufqbba6lcutadapt_out1.fq.gz )
--- local_file
+++ history_data
@@ -1,396 +0,0 @@
-@M01368:8:000000000-A3GHV:1:1101:6911:8255/1
-ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT
-+
-BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB
-@M01368:8:000000000-A3GHV:1:1101:14518:9998/1
-GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT
-+
-AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A//
-@M01368:8:000000000-A3GHV:1:1101:18422:19051/1
-GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG
-+
-CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.
-@M01368:8:000000000-A3GHV:1:1101:25545:21098/1
-ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG
-+
-33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B--
-@M01368:8:000000000-A3GHV:1:1101:5446:12248/1
-AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT
-+
-CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFF
-@M01368:8:000000000-A3GHV:1:1101:5861:6452/1
-ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT
********
*SNIP *
********
->AAAAFFFBFFFGGGGGGGGGGHHFHGHHHHGHHHHHHHHHHHGGGGHHHHFHHHHFHGHHHHGAFFEFHEGHHHHHHHHGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF
-@M01368:8:000000000-A3GHV:1:1113:5741:16959/1
-TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA
-+
-ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0<C;CGGGGEFF/.;0;FFFBF/0;0CFGFFB..9B/;0CBFFBBFFFFBAC?DED9;B9AD;.FFFB/B/;FBA/B//
-@M01368:8:000000000-A3GHV:1:1114:10130:11959/1
-CGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTCTGATCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAACAAACACACATCC
-+
->A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./B/..9.9:...///
-@M01368:8:000000000-A3GHV:1:1114:14540:5315/1
-CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT
-+
-AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE.
-@M01368:8:000000000-A3GHV:1:1114:15066:16302/1
-TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA
-+
-BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<<AHHHGGGGGGGFHH0GHFCCCADGGG?.9/A-???DGGFFF.9F9/EE-;;BBBFFBFFFFFFFFFEFFFFBFFBBFFFFF/BFFBFFFFF-DBFFF;/BFF//BB//9/BEA---9:BFFFFFF/F/.;.:@9.BBFF/;BFF/;/////9/////.
-@M01368:8:000000000-A3GHV:1:1114:16639:15258/1
-CCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT
-+
-11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/;
-@M01368:8:000000000-A3GHV:1:1114:2404:13066/1
-TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC
-+
-CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0

Command Line:

Exit Code:

```
255
```

Standard Error:

FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 2, "input_1": {"values": [{"id": 1418507, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test trinotate 3.2.2+galaxy0 #6)
Problems:
- 'command_line'

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test pangolin 3.1.17+galaxy1 #7)

Problems:

Output json_stats:  different than expected, difference (using diff):
( /tmp/tmpi_1m6c2wcutadapt_rest.json v. /tmp/tmpz2mz3hb_cutadapt_rest.json )
--- local_file
+++ history_data
@@ -2,9 +2,9 @@
   "tag": "Cutadapt report",
   "schema_version": [0, 1],
   "cutadapt_version": "3.5",
-  "python_version": "3.9.7",
+  "python_version": "3.9.10",
   "command_line_arguments": [
-    "-j=1",
+    "-j=10",
     "--json",
     "stats.json",
     "-a",
@@ -17,7 +17,7 @@
     "--action=trim",
     "cutadapt_rest_fa.fa"
   ],
-  "cores": 1,
+  "cores": 10,
   "input": {
     "path1": "cutadapt_rest_fa.fa",
     "path2": null,

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=10 --json stats.json -a AAAGATG --rest-file=rest_output.fa --output=out1.fa --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_rest_fa.fa
Processing reads on 10 cores in single-end mode ...
Finished in 4.33 s (865442 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       5
Reads with adapters:                         5 (100.0%)
Reads written (passing filters):             5 (100.0%)

Total basepairs processed:            97 bp
Total written (filtered):             35 bp (36.1%)

=== Adapter 1 ===

Sequence: AAAGATG; Type: regular 3'; Length: 7; Trimmed: 5 times

Minimum overlap: 3
No. of allowed errors:
1-7 bp: 0

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
7	1	0.0	0	1
12	1	0.0	0	1
14	2	0.0	0	2
15	1	0.0	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94223956, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAGATG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`["rest_file", "json_stats"]`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

❌ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test trim_galore 0.6.7+galaxy0 #10)

Problems:

Job in error state.. tool_id: toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1, exit_code: 255, stderr: FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
.

Output collection 'split_output': expected to have 3 elements, but it had 0.

Command Line:

Exit Code:

```
255
```

Standard Error:

FATAL:   container creation failed: mount /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt->/cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt error: while mounting /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: while getting stat for /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: stat /cvmfs/main.galaxyproject.org/shed_tools/toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/c053d4cad713/cutadapt: input/output error

ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'
ERROR:galaxy.datatypes.registry:Error importing datatype module galaxy.datatypes.wsf
Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 249, in load_datatypes
    module = __import__(datatype_module)
ModuleNotFoundError: No module named 'galaxy.datatypes.wsf'

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 0, "input_1": {"values": [{"id": 94223962, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^GTCGGTAA", "front_adapter_name": "A1", "front_adapter_source_list": "user"}, "single_noindels": "false"}, {"__index__": 1, "front_adapter_source": {"__current_case__": 0, "front_adapter": "^AGGTCACT", "front_adapter_name": "A2", "front_adapter_source_list": "user"}, "single_noindels": "false"}]}, "type": "single"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"multiple_output"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

Passed s

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test tool test #1)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=10 -a AGATCGGAAGAGC --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing reads on 10 cores in single-end mode ...
Finished in 3.18 s (1060202 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94223964, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test racon 1.3.1.1 #11)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=10 -g file:/jetstream/scratch0/main/jobs/41255335/inputs/dataset_d7078a73-699a-4e83-bf2e-0b78346e4d9d.dat --output=split/{name}.fastq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_in_split_fastq_gz.fq.gz
Processing reads on 10 cores in single-end mode ...
Finished in 6.86 s (623358 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                      11
Reads with adapters:                        10 (90.9%)
Reads written (passing filters):            11 (100.0%)

Total basepairs processed:         1,210 bp
Total written (filtered):          1,130 bp (93.4%)

=== Adapter A2 ===

Sequence: AGGTCACT; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5


=== Adapter A1 ===

Sequence: GTCGGTAA; Type: anchored 5'; Length: 8; Trimmed: 5 times

No. of allowed errors: 0

Overview of removed sequences
length	count	expect	max.err	error counts
8	5	0.0	0	5

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94223963, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 94223968, "src": "hda"}]}, "front_adapter_source_list": "file"}, "single_noindels": "false"}]}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"multiple_output"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test mafft 7.221.3 #12)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=10 -a AAAT --untrimmed-output=untrimmed_output.fq --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing reads on 10 cores in single-end mode ...
Finished in 3.40 s (1132265 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)

== Read fate breakdown ==
Reads discarded as untrimmed:                2 (66.7%)
Reads written (passing filters):             1 (33.3%)

Total basepairs processed:           102 bp
Total written (filtered):             30 bp (29.4%)

=== Adapter 1 ===

Sequence: AAAT; Type: regular 3'; Length: 4; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-4 bp: 0

Bases preceding removed adapters:
  A: 0.0%
  C: 100.0%
  G: 0.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
4	1	0.0	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94224565, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AAAT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"untrimmed_file"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test ebi_metagenomics_run_downloader 0.1.0 #13)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=10 -a AGATCGGAAGAGC --untrimmed-output=untrimmed_output.fq.gz --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim bwa-mem-fastq1_fq_gz.fq.gz
Processing reads on 10 cores in single-end mode ...
Finished in 5.38 s (54374 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         2 (2.0%)

== Read fate breakdown ==
Reads discarded as untrimmed:               97 (98.0%)
Reads written (passing filters):             2 (2.0%)

Total basepairs processed:        24,849 bp
Total written (filtered):            496 bp (2.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94224578, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`"untrimmed_file"`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test tp_sort_rows 1.0.0 #15)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=10 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim cutadapt_small_fastq.fq
Processing reads on 10 cores in single-end mode ...
Finished in 2.77 s (922818 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             87 bp (85.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94224656, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test tp_sorted_uniq 1.0.0 #16)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC -u 5 --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --rename={id} barcode={cut_prefix} cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.09 s (31659 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             87 bp (85.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94225020, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "5", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": "{id} barcode={cut_prefix}", "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test hyphy_gard 2.5.31+galaxy1 #17)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=retain cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.04 s (14785 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             80 bp (78.4%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94225295, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "retain", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test prokka 1.14.6+galaxy1 #18)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=mask cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (16932 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
dbkey	`"?"`
__input_ext	`"input"`
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94225295, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "mask", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test build_ucsc_custom_track_1 1.0.0 (+ 1.0.1 once updated on org) #19)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=lowercase cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (16373 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94225323, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "lowercase", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
dbkey	`"?"`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
__input_ext	`"input"`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test roary 3.13.0+galaxy2 #20)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a CGTCCGAANTAG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=none cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (16805 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: CGTCCGAANTAG; Type: regular 3'; Length: 12; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-11 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94225530, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "CGTCCGAANTAG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "none", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test mothur_align_seqs 1.39.5.0 #21)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a TAAACAGATTAGT --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --revcomp cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (15940 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reverse-complemented:                        0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             97 bp (95.1%)

=== Adapter 1 ===

Sequence: TAAACAGATTAGT; Type: regular 3'; Length: 13; Trimmed: 1 times; Reverse-complemented: 0 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 100.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
5	1	0.0	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94225769, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "TAAACAGATTAGT", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "true", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test circos 0.69.8+galaxy7 #26)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (15635 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         1 (33.3%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):             20 bp (19.6%)

=== Adapter 1 ===

Sequence: AGCCGCTANGACG; Type: regular 3'; Length: 13; Trimmed: 1 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 0.0%
  T: 0.0%
  none/other: 100.0%

Overview of removed sequences
length	count	expect	max.err	error counts
34	1	0.0	1	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94226566, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCCGCTANGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 0, "length": "10", "shorten_end": "3prime", "shorten_values": "True"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test table_annovar 0.2 #28)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGCGGCTTAGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --max-expected-errors=10 cutadapt_small_fastq.fq
Processing reads on 6 cores in single-end mode ...
Finished in 0.05 s (15496 µs/read; 0.00 M reads/minute).

=== Summary ===

Total reads processed:                       3
Reads with adapters:                         0 (0.0%)

== Read fate breakdown ==
Reads with too many exp. errors:             0 (0.0%)
Reads written (passing filters):             3 (100.0%)

Total basepairs processed:           102 bp
Total written (filtered):            102 bp (100.0%)

=== Adapter 1 ===

Sequence: AGCGGCTTAGACG; Type: regular 3'; Length: 13; Trimmed: 0 times

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94226784, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGCGGCTTAGACG", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "10", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test circos 0.69.8+galaxy10 #32)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC;noindels -A AGATCGGAAGAGC;noindels --output=/corral4/main/jobs/041/257/41257208/outputs/galaxy_dataset_53fa0027-0465-4f67-ae58-19b1cd122a9d.dat --paired-output=/corral4/main/jobs/041/257/41257208/outputs/galaxy_dataset_5dc84d17-962a-4122-a453-16eba8ddd1fb.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz
Processing reads on 6 cores in paired-end mode ...
Finished in 0.06 s (581 µs/read; 0.10 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       4 (4.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Total written (filtered):         49,677 bp (100.0%)
  Read 1:        24,843 bp
  Read 2:        24,834 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 50.0%
  T: 50.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2
4	1	0.4	0	1
5	1	0.1	0	1

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 2, "input_1": {"values": [{"id": 1418668, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "true"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "true"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": null}, "type": "paired_collection"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test strelka #33)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/corral4/main/jobs/041/257/41257729/outputs/galaxy_dataset_c5465879-ac45-4e13-a4ed-5eee114e7fd4.dat --paired-output=/corral4/main/jobs/041/257/41257729/outputs/galaxy_dataset_15bf6177-9911-43ad-91eb-4b841c1eb721.dat --error-rate=0.1 --times=1 --overlap=3 --action=trim --pair-filter=any --quality-cutoff=5 Unnamed Collection_1.fq.gz Unnamed Collection_2.fq.gz -Q=15,20
Processing reads on 6 cores in paired-end mode ...
Finished in 0.12 s (1198 µs/read; 0.05 M reads/minute).

=== Summary ===

Total read pairs processed:                 99
  Read 1 with adapter:                       2 (2.0%)
  Read 2 with adapter:                       2 (2.0%)
Pairs written (passing filters):            99 (100.0%)

Total basepairs processed:        49,698 bp
  Read 1:        24,849 bp
  Read 2:        24,849 bp
Quality-trimmed:                     747 bp (1.5%)
  Read 1:             0 bp
  Read 2:           747 bp
Total written (filtered):         48,938 bp (98.5%)
  Read 1:        24,843 bp
  Read 2:        24,095 bp

=== First read: Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 50.0%
  G: 50.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	2	1.5	0	2


=== Second read: Adapter 2 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 0.0%
  G: 100.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	1	1.5	0	1
4	1	0.4	0	1

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 2, "input_1": {"values": [{"id": 1418672, "src": "hdca"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "r2": {"adapters2": [{"__index__": 0, "adapter_source2": {"__current_case__": 0, "adapter2": "AGATCGGAAGAGC", "adapter_name2": "", "adapter_source_list2": "user"}, "single_noindels": "false"}], "anywhere_adapters2": [], "cut2": "0", "front_adapters2": [], "quality_cutoff2": "15,20"}, "type": "paired_collection"}
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "5", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test SEACR 1.3+galaxy1 on usegalaxy.org #8)

Command Line:

Exit Code:

```
0
```

Standard Output:

This is cutadapt 3.5 with Python 3.9.10
Command line parameters: -j=6 -a AGATCGGAAGAGC --output=out1.fq.gz --error-rate=0.1 --times=1 --overlap=3 --action=trim --nextseq-trim=20 bwa-mem-fastq1_fq_gz.fq.gz
Processing reads on 6 cores in single-end mode ...
Finished in 0.06 s (620 µs/read; 0.10 M reads/minute).

=== Summary ===

Total reads processed:                      99
Reads with adapters:                         4 (4.0%)
Reads written (passing filters):            99 (100.0%)

Total basepairs processed:        24,849 bp
Quality-trimmed:                     286 bp (1.2%)
Total written (filtered):         24,550 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 4 times

Minimum overlap: 3
No. of allowed errors:
1-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 0.0%
  C: 75.0%
  G: 25.0%
  T: 0.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
3	3	1.5	0	3
4	1	0.4	0	1

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94223960, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "20", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`None`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

✅ toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt (Test Test gffread 2.2.1.3+galaxy0 #9)

Command Line:

Exit Code:

```
0
```

Job Parameters:

Job parameter	Parameter value
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 94223964, "src": "hda"}]}, "r1": {"adapters": [{"__index__": 0, "adapter_source": {"__current_case__": 0, "adapter": "AGATCGGAAGAGC", "adapter_name": "", "adapter_source_list": "user"}, "single_noindels": "false"}], "anywhere_adapters": [], "cut": "0", "front_adapters": []}, "type": "single"}`
adapter_options	`{"action": "trim", "error_rate": "0.1", "internal": "", "match_read_wildcards": " ", "no_indels": "false", "overlap": "3", "revcomp": "false", "times": "1"}`
filter_options	`{"discard_cassava": "false", "discard_trimmed": "false", "discard_untrimmed": "false", "length_R2_options": {"__current_case__": 1, "length_R2_status": "False"}, "max_expected_errors": "", "max_n": "", "maximum_length": "", "minimum_length": "", "pair_filter": "any"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": null, "trim_n": "false", "zero_cap": "false"}`
output_selector	`["report", "info_file"]`
__job_resource	`{"__current_case__": 0, "__job_resource__select": "no"}`
chromInfo	`"/cvmfs/data.galaxyproject.org/managed/len/ucsc/?.len"`
dbkey	`"?"`
__input_ext	`"input"`

jennaj · 2022-03-09T21:26:47Z

/run-tool-test tool_id=toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1

jennaj mentioned this issue Mar 10, 2022

Bug: Cutadapt 3.5+galaxy1 parameter --strip-suffix galaxyproject/usegalaxy-tools#481

Closed

jennaj closed this as completed Mar 16, 2022

mvdbeek mentioned this issue Nov 10, 2022

test cutadapt 4.0+galaxy1 #68

Closed

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Test cutadapt 3.5+galaxy1 #22

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Test cutadapt 3.5+galaxy1 #22

Test cutadapt 3.5+galaxy1 #22

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