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update kmc
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mthang committed Sep 20, 2024
1 parent 3d997eb commit 941d6a5
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211 changes: 170 additions & 41 deletions tools/kmc/kmc.xml
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<tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" >
<description>K-mer counting and filtering of reads</description>
<macros>
<import>macros.xml</import>
</macros>
<xrefs>
<xref type='bio.tools'>kmc</xref>
</xrefs>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<expand macro="stdio" />
<expand macro="version_command" />
<command><![CDATA[
kmc
mkdir output &&
#if $data_type.select == 'individual'
#for $input_file in $data_type.individual_file
#if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
#if $input_file.ext.endswith(".gz")
#set $ext='.fastq.gz'
#else
#set $ext='.fastq'
#end if
ln -s '$input_file' 'in$ext' &&
#elif $input_file.is_of_type("fasta","fasta.gz"):
#if $input_file.ext.endswith(".gz")
#set $ext='.fasta.gz'
#else
#set $ext='.fasta'
#end if
ln -s '$input_file' 'in$ext' &&
#elif $input_file.is_of_type("bam"):
ln -s '$input_file' in.bam &&
#elif $input_file.is_of_type("kmc_suf"):
#if $input_file.ext.endswith(".kmc_suf")
#set $suf_ext='.kmc_suf'
#end if
#if $input_file.ext.endswith(".kmc_pre")
#set $pre_ext='.kmc_pre'
#end if
ln -s '$input_file' 'in$suf_ext' &&
ln -s '$input_file' 'in$pre_ext' &&
#end if
#end for
#else
mkdir input_dir &&
#import re
#for $input_file in $data_type.collection_file
#if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
#if $input_file.ext.endswith(".gz")
#set $ext='.fastq.gz'
#else
#set $ext='.fastq'
#end if
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
ln -s '$input_file' 'input_dir/${identifier}' &&
#elif $input_file.is_of_type("fasta","fasta.gz"):
#if $input_file.ext.endswith(".gz")
#set $ext='.fasta.gz'
#else
#set $ext='.fasta'
#end if
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
ln -s '$input_file' 'input_dir/${identifier}' &&
#elif $input_file.is_of_type("bam"):
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
ln -s '$input_file' 'input_dir/${identifier}' &&
#elif $input_file.is_of_type("kmc_suf"):
#if $input_file.ext.endswith(".kmc_suf")
#set $suf_ext='.kmc_suf'
#end if
#if $input_file.ext.endswith(".kmc_pre")
#set $pre_ext='.kmc_pre'
#end if
#set $identifier = re.sub('[^\s\w\-\\.]', '_', str($input_file.element_identifier))
ln -s '$input_file' 'input_dir/${identifier}' &&
ln -s '$input_file' 'input_dir/${identifier}' &&
#end if
#end for
ls -ld input_dir/* | awk '{print $9}' >> files.list &&
#end if
kmc
-t\${GALAXY_SLOTS:-4}
#if $params.k:
-k'$params.k'
Expand All @@ -21,71 +89,132 @@
#if $params.j:
-j'$statistic'
#end if
#if $params.exclude_length:
-ci'$params.exclude_length'
#if $params.p:
-p'$params.p'
#end if
#if $params.ci:
-ci'$params.ci'
#end if
#if $params.max_counter_value:
-cs'$params.max_counter_value'
#if $params.cs:
-cs'$params.cs'
#end if
#if $input_file.is_of_type("fastq"):
-fq
#elif $input_file.is_of_type("fasta"):
-fm
#if $params.cx:
-cx'$params.cx'
#end if
#if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
-fq
#elif $input_file.is_of_type("fasta","fasta.gz"):
#if $data_type.select == "individual":
-fa
#else
-fm
#end if
#elif $input_file.is_of_type("bam"):
-fbam
-fbam
#elif $input_file.is_of_type("kmc_suf"):
-fkmc
-fkmc
#end if
#if $input_file.is_of_type('fastq.gz','fasta.gz','fastqsanger.gz'):
-f
#end if
$input_file
db
.
#if $data_type.select == 'individual'
#if $input_file.is_of_type("fastq","fastq.gz","fastqsanger.gz"):
#if $input_file.ext.endswith(".gz")
in.fastq.gz
#else
in.fastq
#end if
#elif $input_file.is_of_type("fasta","fasta.gz"):
#if $input_file.ext.endswith(".gz")
in.fasta.gz
#else
in.fasta
#end if
#elif $input_file.is_of_type("bam"):
in.bam
#end if
#else
@files.list
#end if
output/kmer_"$params.k"
.
]]></command>
<inputs>
<expand macro="macro_input" />
<section name="params" title="parameter" expanded="false">
<param argument="-k" type="integer" value="25" label="k-mer length (k from 1 to 256; default: 25)" />
<param argument="-m" type="integer" value="12" label="max amount of RAM in GB (from 1 to 1024); default: 12" />
<param name="signature_length" arguments="-p" type="integer" value="9" label="signature length (5, 6, 7, 8, 9, 10, 11); default: 9"/>
<param name="exclude_length" arguments="-ci" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/>
<param name="max_counter_value" arguments="-cs" type="integer" value="255" label="maximal value of a counter (default: 255)"/>
<param name="exclude_kmer_occurence" arguments="-cx" type="integer" value="1000000000" label="xclude k-mers occurring more of than [value] times (default: 1e9)"/>
<param argument="-p" type="integer" value="9" label="signature length (5, 6, 7, 8, 9, 10, 11); default: 9"/>
<param argument="-ci" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/>
<param argument="-cs" type="integer" value="255" label="maximal value of a counter (default: 255)"/>
<param argument="-cx" type="integer" value="1000000000" label="xclude k-mers occurring more of than [value] times (default: 1e9)"/>
<param argument="-j" type="boolean" truevalue="-j" falsevalue="" checked="True" label="file name with execution summary in JSON format"/>
</section>
</inputs>
<outputs>
<data format="json" name="statistic" label="${tool.name} on ${on_string}">
<filter>params['j']</filter>
</data>
<data format="json" name="statistic" label="${tool.name} on ${on_string}">
<filter>params['j']</filter>
</data>
<collection name="kmc_db" type="list" label="${tool.name} on ${on_string}: kmc db">
<data format="binary" name="db.kmc_suf" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_suf" />
<data format="binary" name="db.kmc_pre" label="${tool.name} on ${on_string}" from_work_dir="db.kmc_pre" />
<discover_datasets pattern="(?P&lt;designation&gt;.+)" directory="output" format="binary" />
</collection>
</outputs>

<tests>
<test>
<!-- #1 test fastq with common parameters -->
<param name="input_file" value="F3D0_R1.fastq" ftype="fastq"/>
<!-- output file is too large for testing; comment out to test on local machine with update_test_data option -->
<!-- <test expect_num_outputs="2"> -->
<!-- #1 test individual fastq with common parameters -->
<!-- <param name="individual_file" value="filtered_1.fastq" ftype="fastq"/>
<param name="k" value="25" />
<param name="m" value="12" />
<param name="p" value="9" />
<param name="ci" value="2" />
<param name="cs" value="255" />
<output name="db.kmc_suf" file="db.kmc_suf" ftype="binary" />
<output name="db.kmc_pre" file="db.kmc_pre" ftype="binary" />
</test>
<test>
<!-- #2 test fasta with common parameters -->
<param name="input_file" value="contigs.fa" ftype="fasta"/>
<param name="cs" value="255" />
<output_collection name="kmc_db" type="list">
<element name="kmer_25.kmc_pre" file="kmer_25.kmc_pre" ftype="binary" />
<element name="kmer_25.kmc_suf" file="kmer_25.kmc_suf" ftype="binary" />
</output_collection>
<output name="statistic" file="statistic_25.json" ftype="json"/>
</test> -->
<test expect_num_outputs="2">
<!-- #2 test individual fasta with common parameters -->
<param name="individual_file" value="test.fasta.gz" ftype="fasta.gz"/>
<param name="k" value="27" />
<param name="m" value="24" />
<param name="ci" value="2" />
<param name="cs" value="255" />
<param name="fm" value="-fm" />
<output name="contig_kmer27.kmc_suf" file="contig_kmer27.kmc_suf" ftype="binary" />
<output name="contig_kmer27.kmc_pre" file="contig_kmer27.kmc_pre" ftype="binary" />
</test>
<output_collection name="kmc_db" type="list">
<element name="kmer_27.kmc_suf" file="kmer_27.kmc_suf" ftype="binary" />
<element name="kmer_27.kmc_pre" file="kmer_27.kmc_pre" ftype="binary" />
</output_collection>
<output name="statistic" file="statistic_27.json" ftype="json"/>
</test>
<!-- output file is too large for testing; comment out to test on local machine -->
<!-- <test expect_num_outputs="2"> -->
<!-- #3 test collection fastq with common parameters -->
<!-- <param name="k" value="29" />
<param name="m" value="12" />
<param name="p" value="9" />
<param name="ci" value="2" />
<param name="cs" value="255" />
<conditional name="data_type">
<param name="select" value="collection"/>
<param name="collection_file">
<collection type="list">
<element name="filtered_1.fastq" value="filtered_1.fastq" ftype="fastq"/>
<element name="filtered_2.fastq" value="filtered_2.fastq" ftype="fastq"/>
</collection>
</param>
</conditional>
<output_collection name="kmc_db">
<element name="kmer_29.kmc_suf" file="kmer_29.kmc_suf" ftype="binary" />
<element name="kmer_29.kmc_pre" file="kmer_29.kmc_pre" ftype="binary" />
</output_collection>
<output name="statistic" file="statistic_collection.json" ftype="json"/>
</test>
-->
</tests>
<help><![CDATA[
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13 changes: 12 additions & 1 deletion tools/kmc/macros.xml
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Expand Up @@ -18,7 +18,18 @@
]]></version_command>
</xml>
<xml name="macro_input">
<param name="input_file" type="data" format="fasta,fastq,fasta.gz,fastqsanger,fastq.gz,bam" label="Sequence file"/>
<conditional name="data_type">
<param name="select" type="select" label="File input type for KMC">
<option value="individual">In individual datasets</option>
<option value="collection">In collection</option>
</param>
<when value="individual">
<param name="individual_file" type="data" format="fasta,fastq,fasta.gz,fastqsanger,fastqsanger.gz,fastq.gz,bam" multiple="true" label="FASTQ/A file"/>
</when>
<when value="collection">
<param name="collection_file" type="data_collection" collection_type="list" format="fasta,fastq,fasta.gz,fastqsanger,fastqsanger.gz,fastq.gz,bam" label="A list of FASTQ/A files"/>
</when>
</conditional>
</xml>
<xml name="general_option">
<param argument="exclude_length" type="integer" value="2" label="exclude k-mers occurring less than [value] times (default: 2)"/>
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15 changes: 15 additions & 0 deletions tools/kmc/test-data/statistic_27.json
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{
"1st_stage": "0.06634s",
"2nd_stage": "1.20152s",
"Total": "1.26786s",
"Tmp_size": "0MB",
"Stats": {
"#k-mers_below_min_threshold": 124352,
"#k-mers_above_max_threshold": 0,
"#Unique_k-mers": 186071,
"#Unique_counted_k-mers": 61719,
"#Total no. of k-mers": 283537,
"#Total_reads": 2,
"#Total_super-k-mers": 26721
}
}
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