Mercurial > repos > galaxy-australia > kmc
changeset 1:c7fda6e88567 draft default tip
planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/kmc commit 3be367228b531c346c10700f07d57ae44394be36-dirty
| author | galaxy-australia |
|---|---|
| date | Tue, 01 Oct 2024 04:06:26 +0000 |
| parents | ca2743037241 |
| children | |
| files | kmc.xml kmc_tools_filter.xml kmc_tools_simple.xml kmc_tools_transform.xml macros.xml test-data/Illumina.1.fastq.gz test-data/Illumina.2.fastq.gz test-data/db.kmc_pre test-data/db.kmc_suf test-data/kmer_27.kmc_pre test-data/kmer_27.kmc_suf test-data/statistic_27.json_bk test-data/test.fasta.gz |
| diffstat | 13 files changed, 225 insertions(+), 56 deletions(-) [+] |
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--- a/kmc.xml Tue Sep 27 05:20:06 2022 +0000 +++ b/kmc.xml Tue Oct 01 04:06:26 2024 +0000 @@ -1,91 +1,233 @@ -<tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > +<tool id="kmc" name="KMC Counter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <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' #end if - #if $params.m: - -m'$params.m' - #end if + -m\${GALAXY_MEMORY_GB:-4} #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 $params.cs: + -cs'$params.cs' + #end if + #if $params.cx: + -cx'$params.cx' #end if - #if $params.max_counter_value: - -cs'$params.max_counter_value' + #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 + #elif $input_file.is_of_type("kmc_suf"): + -fkmc #end if - #if $input_file.is_of_type("fastq"): - -fq - #elif $input_file.is_of_type("fasta"): - -fm - #elif $input_file.is_of_type("bam"): - -fbam - #elif $input_file.is_of_type("kmc_suf"): - -fkmc + + #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 ${on_string}"> - <filter>params['j']</filter> - </data> + <data name="statistic" format="json" label="${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<designation>.+)" directory="output" format="binary" /> </collection> </outputs> - <tests> - <test> - <!-- #1 test fastq with common parameters --> - <param name="input_file" value="F3D0_R1.fastq" ftype="fastq"/> + <test expect_num_outputs="2"> + <!-- #1 test individual fasta file --> + <param name="individual_file" value="test.fasta.gz" ftype="fasta.gz"/> + <param name="k" value="27" /> + <param name="ci" value="2" /> + <param name="cs" value="255" /> + <output_collection name="kmc_db" type="list"> + <element name="kmer_27.kmc_pre" file="kmer_27.kmc_pre" ftype="binary" /> + <element name="kmer_27.kmc_suf" file="kmer_27.kmc_suf" ftype="binary" /> + </output_collection> + <output name="statistic" ftype="json"> + <assert_contents> + <has_text text="1st_stage"/> + <has_text text="2nd_stage"/> + <has_text text="Stats"/> + </assert_contents> + </output> + </test> + <!-- output file is too large for testing; comment out to test on local machine with update_test_data option --> + <!-- <test expect_num_outputs="2"> --> + <!-- #2 test individual fastq file --> + <!-- <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="k" value="27" /> - <param name="m" value="24" /> + <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" ftype="json"> + <assert_contents> + <has_text text="1st_stage"/> + <has_text text="2nd_stage"/> + <has_text text="Stats"/> + </assert_contents> + </output> + </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" /> - <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> + <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" ftype="json"> + <assert_contents> + <has_text text="1st_stage"/> + <has_text text="2nd_stage"/> + <has_text text="Stats"/> + </assert_contents> + </output> + </test> + --> </tests> <help><![CDATA[
--- a/kmc_tools_filter.xml Tue Sep 27 05:20:06 2022 +0000 +++ b/kmc_tools_filter.xml Tue Oct 01 04:06:26 2024 +0000 @@ -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>
--- a/kmc_tools_simple.xml Tue Sep 27 05:20:06 2022 +0000 +++ b/kmc_tools_simple.xml Tue Oct 01 04:06:26 2024 +0000 @@ -1,4 +1,4 @@ -<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>
--- a/kmc_tools_transform.xml Tue Sep 27 05:20:06 2022 +0000 +++ b/kmc_tools_transform.xml Tue Oct 01 04:06:26 2024 +0000 @@ -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>
--- a/macros.xml Tue Sep 27 05:20:06 2022 +0000 +++ b/macros.xml Tue Oct 01 04:06:26 2024 +0000 @@ -1,6 +1,7 @@ <macros> <token name="@TOOL_VERSION@">3.2.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> + <token name="@PROFILE@">22.05</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">kmc</requirement> @@ -18,7 +19,18 @@ ]]></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)"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/statistic_27.json_bk Tue Oct 01 04:06:26 2024 +0000 @@ -0,0 +1,15 @@ +{ + "1st_stage": "0.077217s", + "2nd_stage": "1.20559s", + "Total": "1.28281s", + "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 + } +}