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Merge pull request #140 from mthang/kmc_update
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update kmc test-data and wrapper
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@mthang
mthang authored Oct 2, 2024
2 parents 8222cf2 + 968ec9c commit 22dae12
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Showing 52 changed files with 30,428 additions and 87,961 deletions.
2 changes: 1 addition & 1 deletion tools/kmc/kmc.xml
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Expand Up @@ -162,7 +162,7 @@
<tests>
<test expect_num_outputs="2">
<!-- #1 test individual fasta file -->
<param name="individual_file" value="test.fasta.gz" ftype="fasta.gz"/>
<param name="individual_file" value="test.fasta" ftype="fasta"/>
<param name="k" value="27" />
<param name="ci" value="2" />
<param name="cs" value="255" />
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14 changes: 7 additions & 7 deletions tools/kmc/kmc_tools_filter.xml
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@@ -1,4 +1,4 @@
<tool id="kmc_filter" name="KMC filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
<tool id="kmc_filter" name="KMC filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>filtering KMC's database</description>
<xrefs>
<xref type='bio.tools'>kmc</xref>
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<!-- #1 test with common parameters -->
<param name="input_collection">
<collection type="list">
<element name="db.kmc_suf" value="db.kmc_suf" dbkey="89"/>
<element name="db.kmc_pre" value="db.kmc_pre" dbkey="89"/>
<element name="db.kmc_pre" value="filtered_kmers1.kmc_pre" dbkey="89"/>
<element name="db.kmc_suf" value="filtered_kmers1.kmc_suf" dbkey="89"/>
</collection>
</param>
<param name="input_read_file" value="F3D0_R1.fastq" ftype="fastq"/>
<param name="input_read_file" value="Illumina.1.fastq" ftype="fastq"/>
<param name="min_kmer_occurrence" value="3" />
<param name="exclude_length" value="2" />
<param name="exclude_kmer_occurence" value="10" />
Expand All @@ -86,11 +86,11 @@
<!-- #2 test with common parameters -->
<param name="input_collection">
<collection type="list">
<element name="db.kmc_suf" value="db.kmc_suf" dbkey="89"/>
<element name="db.kmc_pre" value="db.kmc_pre" dbkey="89"/>
<element name="db.kmc_pre" value="filtered_kmers2.kmc_pre" dbkey="89"/>
<element name="db.kmc_suf" value="filtered_kmers2.kmc_suf" dbkey="89"/>
</collection>
</param>
<param name="input_read_file" value="F3D0_R1.fastq" ftype="fastq"/>
<param name="input_read_file" value="Illumina.2.fastq" ftype="fastq"/>
<param name="exclude_length" value="10" />
<param name="exclude_kmer_occurence" value="100" />
<output name="filtered_2.fastq" file="filtered_2.fastq" ftype="fastq" />
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61 changes: 32 additions & 29 deletions tools/kmc/kmc_tools_simple.xml
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@@ -1,11 +1,11 @@
<tool id="kmc_simple" name="KMC simple" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
<tool id="kmc_simple" name="KMC simple" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>simple operations for two input kmer sets</description>
<xrefs>
<xref type='bio.tools'>kmc</xref>
</xrefs>
<macros>
<import>macros.xml</import>
</macros>
<xrefs>
<xref type='bio.tools'>kmc</xref>
</xrefs>
<expand macro="requirements" />
<expand macro="stdio" />
<expand macro="version_command" />
Expand Down Expand Up @@ -222,14 +222,14 @@
<!-- #1 test with default parameters -->
<param name="input_collection_one">
<collection type="list">
<element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/>
<element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/>
<element name="kmers_one.kmc_pre" value="filtered_kmers1.kmc_pre"/>
<element name="kmers_one.kmc_suf" value="filtered_kmers1.kmc_suf"/>
</collection>
</param>
<param name="input_collection_two">
<collection type="list">
<element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/>
<element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/>
<element name="kmers_two.kmc_pre" value="filtered_kmers2.kmc_pre"/>
<element name="kmers_two.kmc_suf" value="filtered_kmers2.kmc_suf"/>
</collection>
</param>
<conditional name="input_options_cond">
Expand All @@ -240,22 +240,22 @@
<param name="oc" value="max"/>
</section>
<output_collection name="kmc_db" type="list">
<element name="intersect_max_db.kmc_suf" file="intersect_max_db.kmc_suf"/>
<element name="intersect_max_db.kmc_pre" file="intersect_max_db.kmc_pre"/>
<element name="intersect_max_db.kmc_suf" file="intersect_max_db.kmc_suf"/>
</output_collection>
</test>
<test>
<!-- #2 test with input parameters for KMC DB one only -->
<param name="input_collection_one">
<collection type="list">
<element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/>
<element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/>
<element name="kmers_one.kmc_pre" value="filtered_kmers1.kmc_pre"/>
<element name="kmers_one.kmc_suf" value="filtered_kmers1.kmc_suf"/>
</collection>
</param>
<param name="input_collection_two">
<collection type="list">
<element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/>
<element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/>
<element name="kmers_two.kmc_pre" value="filtered_kmers2.kmc_pre"/>
<element name="kmers_two.kmc_suf" value="filtered_kmers2.kmc_suf"/>
</collection>
</param>
<conditional name="input_options_cond">
Expand All @@ -270,22 +270,22 @@
<param name="oc" value="min"/>
</section>
<output_collection name="kmc_db" type="list">
<element name="intersect_min_db.kmc_suf" file="intersect_min_db.kmc_suf"/>
<element name="intersect_min_db.kmc_pre" file="intersect_min_db.kmc_pre"/>
<element name="intersect_min_db.kmc_suf" file="intersect_min_db.kmc_suf"/>
</output_collection>
</test>
<test>
<!-- #3 test with input parameters for KMC DB two only -->
<param name="input_collection_one">
<collection type="list">
<element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/>
<element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/>
<element name="kmers_one.kmc_pre" value="filtered_kmers1.kmc_pre"/>
<element name="kmers_one.kmc_suf" value="filtered_kmers1.kmc_suf"/>
</collection>
</param>
<param name="input_collection_two">
<collection type="list">
<element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/>
<element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/>
<element name="kmers_two.kmc_pre" value="filtered_kmers2.kmc_pre"/>
<element name="kmers_two.kmc_suf" value="filtered_kmers2.kmc_pre"/>
</collection>
</param>
<conditional name="input_options_cond">
Expand All @@ -295,44 +295,47 @@
<section name="kmc_db_two_param">
<param name="min_kmer_occurrence" value="3"/>
<param name="max_kmer_occurrence" value="30"/>
</section>
<section name="add_output_params">
<param name="oc" value="sum"/>
</section>
<output_collection name="kmc_db" type="list">
<element name="union_db.kmc_suf" file="union_db.kmc_suf"/>
<element name="union_db.kmc_pre" file="union_db.kmc_pre"/>
<element name="union_sum_db.kmc_pre" file="union_sum_db.kmc_pre"/>
<element name="union_sum_db.kmc_suf" file="union_sum_db.kmc_suf"/>
</output_collection>
</test>
<test>
<!-- #4 test with input parameters for both KMC DB -->
<param name="input_collection_one">
<collection type="list">
<element name="kmers_one.kmc_suf" value="kmers_one.kmc_suf"/>
<element name="kmers_one.kmc_pre" value="kmers_one.kmc_pre"/>
<element name="kmers_one.kmc_pre" value="filtered_kmers1.kmc_pre"/>
<element name="kmers_one.kmc_suf" value="filtered_kmers1.kmc_pre"/>
</collection>
</param>
<param name="input_collection_two">
<collection type="list">
<element name="kmers_two.kmc_suf" value="kmers_two.kmc_suf"/>
<element name="kmers_two.kmc_pre" value="kmers_two.kmc_pre"/>
<element name="kmers_two.kmc_pre" value="filtered_kmers2.kmc_pre"/>
<element name="kmers_two.kmc_suf" value="filtered_kmers2.kmc_suf"/>
</collection>
</param>
<conditional name="input_options_cond">
<param name="input_param" value="both_kmc_params"/>
</conditional>
<param name="select_operation" value="counters_subtract" />
<section name="both_db_one_param">
<param name="min_kmer_occurrence" value="2"/>
<param name="max_kmer_occurrence" value="20"/>
<param name="min_kmer_occurrence" value="1"/>
<param name="max_kmer_occurrence" value="10"/>
</section>
<section name="both_db_two_param">
<param name="min_kmer_occurrence" value="3"/>
<param name="max_kmer_occurrence" value="30"/>
<param name="min_kmer_occurrence" value="2"/>
<param name="max_kmer_occurrence" value="20"/>
</section>
<section name="add_output_params">
<param name="oc" value="sum"/>
</section>
<output_collection name="kmc_db" type="list">
<element name="counters_subtract_sum_db.kmc_suf" file="counters_subtract_sum_db.kmc_suf"/>
<element name="counters_subtract_sum_db.kmc_pre" file="counters_subtract_sum_db.kmc_pre"/>
<element name="counters_subtract_sum_db.kmc_suf" file="counters_subtract_sum_db.kmc_suf"/>
</output_collection>
</test>
</tests>
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30 changes: 15 additions & 15 deletions tools/kmc/kmc_tools_transform.xml
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@@ -1,4 +1,4 @@
<tool id="kmc_transform" name="KMC transform" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
<tool id="kmc_transform" name="KMC transform" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description>single KMC's database</description>
<xrefs>
<xref type='bio.tools'>kmc</xref>
Expand Down Expand Up @@ -136,8 +136,8 @@
<!-- #1 test perform sort operation on KMC DB -->
<param name="input_collection">
<collection type="list">
<element name="db.kmc_suf" value="db.kmc_suf"/>
<element name="db.kmc_pre" value="db.kmc_pre"/>
<element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
<element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
</collection>
</param>
<conditional name="ops">
Expand All @@ -160,8 +160,8 @@
<!-- #2 test Generate Histogram Table -->
<param name="input_collection">
<collection type="list">
<element name="db.kmc_suf" value="db.kmc_suf"/>
<element name="db.kmc_pre" value="db.kmc_pre"/>
<element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
<element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
</collection>
</param>
<conditional name="ops">
Expand All @@ -183,8 +183,8 @@
<!-- #3 test Generate dump Table -->
<param name="input_collection">
<collection type="list">
<element name="db.kmc_suf" value="db.kmc_suf"/>
<element name="db.kmc_pre" value="db.kmc_pre"/>
<element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
<element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
</collection>
</param>
<conditional name="ops">
Expand All @@ -206,8 +206,8 @@
<!-- #4 test perform reduce operation -->
<param name="input_collection">
<collection type="list">
<element name="db.kmc_suf" value="db.kmc_suf"/>
<element name="db.kmc_pre" value="db.kmc_pre"/>
<element name="db.kmc_pre" value="filtered_kmers1.kmc_pre"/>
<element name="db.kmc_suf" value="filtered_kmers1.kmc_suf"/>
</collection>
</param>
<repeat name="operations">
Expand Down Expand Up @@ -237,13 +237,13 @@
<param name="max_kmer_occurrence" value="40"/>
</section>
</repeat>
<output_collection name="kmc_db" type="list">
<element name="reduce_1_db.kmc_suf" file="reduce_1_db.kmc_suf"/>
<element name="reduce_1_db.kmc_pre" file="reduce_1_db.kmc_pre"/>
<element name="sort_2_db.kmc_suf" file="sort_2_db.kmc_suf"/>
<element name="sort_2_db.kmc_pre" file="sort_2_db.kmc_pre"/>
<output_collection name="kmc_db" type="list">
<element name="compact_3_db.kmc_pre" file="compact_3_db.kmc_pre"/>
<element name="compact_3_db.kmc_suf" file="compact_3_db.kmc_suf"/>
<element name="compact_3_db.kmc_pre" file="compact_3_db.kmc_pre"/>
<element name="reduce_1_db.kmc_pre" file="reduce_1_db.kmc_pre"/>
<element name="reduce_1_db.kmc_suf" file="reduce_1_db.kmc_suf"/>
<element name="sort_2_db.kmc_pre" file="sort_2_db.kmc_pre"/>
<element name="sort_2_db.kmc_suf" file="sort_2_db.kmc_suf"/>
</output_collection>
</test>
</tests>
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2 changes: 1 addition & 1 deletion tools/kmc/macros.xml
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Expand Up @@ -95,7 +95,7 @@
<param name="min_kmer_occurrence" argument="-ci" type="integer" optional="true" label="exclude k-mers occurring less than x times"/>
<param name="max_kmer_occurrence" argument="-cx" type="integer" optional="true" label="exclude k-mers occurring more of than x times"/>
<param name="max_counter_value" argument="-cs" type="integer" optional="true" label="maximal value of a counter"/>
<param argument="-oc" name="oc" type="select" optional="true" label="Counter Calculation" help="redefine counter calculation mode for equal k-mers">
<param argument="-oc" type="select" optional="true" label="Counter Calculation" help="redefine counter calculation mode for equal k-mers">
<option value="min">min - get lower value of a k-mer counter</option>
<option value="max">max - get upper value of a k-mer counter</option>
<option value="sum">sum - get sum of counters from both databases</option>
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