Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5

natefoo · 2021-12-07T17:39:53Z

This tool is already configured to run in Singularity.

Installed in galaxyproject/usegalaxy-tools#447.

natefoo · 2021-12-07T17:41:49Z

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

mvdbeek · 2021-12-07T17:50:55Z

Results (powered by Planemo)

Summary

State	Count
Total	33
Passed	16
Error	0
Failure	17
Skipped	0

Failed s

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

Problems:

500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b52737edec0d7b5017/display?raw=true

500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b55d68d51f66b31dc3/display?raw=true

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 (685 µs/read; 0.09 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": 82414150, "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": "", "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_search_rest_results 0.1.1 #14)
Problems:
- 'command_line'

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

Problems:

500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b54859691d43363960/display?raw=true

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 (17795 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": 82414168, "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": "", "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)

Problems:

500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b5095affee7746ddd5/display?raw=true

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 0.05 s (15558 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": 82414168, "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": "", "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 #3)
Problems:
- 'command_line'

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

Problems:

500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b55f3c5cb058e65dc5/display?raw=true

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 (16225 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": 82414173, "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": "", "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 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 circos 0.69.8+galaxy10 #32)

Problems:

500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b58df200d35f819c9e/display?raw=true

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/039/500/39500616/outputs/galaxy_dataset_0b0afb4f-7ed9-465d-b422-dee7ab935459.dat --paired-output=/corral4/main/jobs/039/500/39500616/outputs/galaxy_dataset_2f221778-e5fe-4c5a-8d28-bf0d67ec49db.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 (576 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": 1297650, "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": "", "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)

Problems:

500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b5b9acd9f3a4dff170/display?raw=true

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/039/500/39500617/outputs/galaxy_dataset_54657fb0-abd4-4bca-92e0-eabe97d7ba7c.dat --paired-output=/corral4/main/jobs/039/500/39500617/outputs/galaxy_dataset_b8be6988-fff6-4d15-ba36-8ca760987220.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 (542 µs/read; 0.11 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": 1297652, "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": "", "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:

500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b542f6d0b6113aa73d/display?raw=true

500 Server Error: Internal Server Error for url: https://usegalaxy.org/api/histories/f9ed30e8defc1cae/contents/bbd44e69cb8906b55dec41fc9b98dbda/display?raw=true

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 0.07 s (13356 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": 82414107, "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": "", "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: None, stderr: .

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

Command Line:

Job Parameters:

Job parameter	Parameter value
library	{"__current_case__": 0, "input_1": {"values": [{"id": 82414111, "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": "", "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 3.9.7
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 0.05 s (17418 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": 82414112, "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": "", "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 0.06 s (583 µs/read; 0.10 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": 82414115, "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": "", "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/6/2/a/dataset_62a4f69b-f0e1-41b3-96e5-8a400d8988a8.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 0.09 s (8218 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": 82414109, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 82414116, "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": "", "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 0.04 s (14824 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": 82414154, "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": "", "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 0.06 s (20588 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": 82414154, "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": "", "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 0.06 s (18753 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": 82414168, "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": "", "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 0.04 s (14071 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": 82414173, "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": "", "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 0.06 s (19612 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": 82414173, "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": "", "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 0.10 s (34787 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": 82414201, "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": "", "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 0.04 s (14993 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": 82414201, "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": "", "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 0.05 s (16027 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": 82414201, "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": "", "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/039/500/39500551/outputs/galaxy_dataset_5b78f082-379b-4c9a-ae9d-b81ecb00789e.dat --paired-output=/corral4/main/jobs/039/500/39500551/outputs/galaxy_dataset_e49000c2-f7a2-47b6-85ff-8280ecefb317.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 (517 µs/read; 0.12 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": 1297646, "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": "", "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 0.06 s (560 µs/read; 0.11 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": 82414115, "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": "", "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": 82414112, "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": "", "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"`

natefoo · 2021-12-07T18:28:26Z

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

Increased download attempts from 2 to 32, which is what I've been using when testing from the command line.

mvdbeek · 2021-12-07T19:17:50Z

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/tmp5il6xfercutadapt_rest.json v. /tmp/tmpnujq0u4wcutadapt_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 0.10 s (20545 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
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"}`
library	`{"__current_case__": 0, "input_1": {"values": [{"id": 82415310, "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"}`
read_mod_options	`{"length_tag": null, "nextseq_trim": "0", "quality_cutoff": "0", "rename": null, "shorten_options": {"__current_case__": 1, "shorten_values": "False"}, "strip_suffix": "", "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=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 1.14 s (379415 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": 82415315, "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": "", "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=10 -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 10 cores in single-end mode ...
Finished in 6.02 s (60818 µs/read; 0.00 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": 82415314, "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": "", "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=10 -g file:/jetstream/scratch0/main/jobs/39501486/inputs/dataset_0e94daef-475e-4d53-a713-a1435abc1da8.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 7.78 s (706942 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": 82415311, "src": "hda"}]}, "r1": {"adapters": [], "anywhere_adapters": [], "cut": "0", "front_adapters": [{"__index__": 0, "front_adapter_source": {"__current_case__": 2, "front_adapter_file": {"values": [{"id": 82415316, "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": "", "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 0.05 s (18025 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": 82415347, "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": "", "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 0.10 s (974 µs/read; 0.06 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": 82415407, "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": "", "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=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 2.89 s (962239 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": 82415538, "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": "", "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=10 -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 10 cores in single-end mode ...
Finished in 9.52 s (3172845 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": 82415538, "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": "", "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 0.07 s (22246 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": 82415548, "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": "", "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 (18062 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": 82415569, "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": "", "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 0.08 s (26085 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": 82415569, "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": "", "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 0.06 s (18497 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": 82415607, "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": "", "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 (16905 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": 82415607, "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": "", "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=10 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=10 cutadapt_small_fastq.fq
Processing reads on 10 cores in single-end mode ...
Finished in 1.40 s (467154 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": 82415804, "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": "", "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=10 -a AGCCGCTANGACG --output=out1.fq --error-rate=0.1 --times=1 --overlap=3 --action=trim --length=-10 cutadapt_small_fastq.fq
Processing reads on 10 cores in single-end mode ...
Finished in 5.11 s (1704897 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": 82415888, "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": "", "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 0.08 s (28167 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": 82415900, "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": "", "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=10 -a AGATCGGAAGAGC -A AGATCGGAAGAGC --output=/jetstream/scratch0/main/jobs/39501485/outputs/dataset_2eb82c17-e5fd-4786-8aaa-817dca189e10.dat --paired-output=/jetstream/scratch0/main/jobs/39501485/outputs/dataset_d2e7c738-bd09-48d7-927a-6093d81dea6f.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 10 cores in paired-end mode ...
Finished in 3.05 s (30846 µs/read; 0.00 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": 1297774, "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": "", "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/039/501/39501903/outputs/galaxy_dataset_0ea0da83-76eb-4b1b-acf2-2bce3ef34418.dat --paired-output=/corral4/main/jobs/039/501/39501903/outputs/galaxy_dataset_605d6210-69b8-4b4d-ad27-bd06f083b9e1.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 0.09 s (885 µs/read; 0.07 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": 1297822, "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": "", "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/039/501/39501922/outputs/galaxy_dataset_ee483ce3-e654-4f72-80c4-e51c64109d0c.dat --paired-output=/corral4/main/jobs/039/501/39501922/outputs/galaxy_dataset_f7968f4d-e42f-410b-9a3a-d0cefda338da.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 0.10 s (1029 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": 1297824, "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": "", "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 0.11 s (1068 µs/read; 0.06 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": 82415314, "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": "", "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": 82415315, "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": "", "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 0.05 s (4680 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": 82415308, "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": "", "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"`

natefoo · 2021-12-07T20:54:52Z

 Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/galaxy/tool_util/verify/script.py", line 297, in run_test
    register_job_data=register, publish_history=publish_history, **verify_kwds
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 1134, in verify_tool
    raise e
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 1127, in verify_tool
    job_stdio = _verify_outputs(testdef, test_history, jobs, data_list, data_collection_list, galaxy_interactor, quiet=quiet)
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/site-packages/galaxy/tool_util/verify/interactor.py", line 1271, in _verify_outputs
    raw_data = job_stdio[what]
KeyError: 'command_line'

Maybe an issue with the galaxy-tool-util version? Because this doesn't happen locally. I'm declaring this working since it passes tests when I run those tests locally (against Main) from the command line.

natefoo closed this as completed Dec 7, 2021

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Test gffread 2.2.1.3+galaxy0 #9

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Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5

Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5

natefoo commented Dec 7, 2021

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Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5

Test toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/3.5+galaxy1 #5

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