Mercurial > repos > iuc > rasusa
changeset 3:add156116c63 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rasusa commit 3a1b13f3f0845f60b4a023fd547a9d2ad0170072
| author | iuc |
|---|---|
| date | Wed, 10 Jul 2024 17:01:16 +0000 |
| parents | c8f1cd6c1fbf |
| children | |
| files | rasusa.xml test-data/input.bam test-data/output.bam |
| diffstat | 3 files changed, 108 insertions(+), 66 deletions(-) [+] |
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--- a/rasusa.xml Wed Feb 28 15:16:59 2024 +0000 +++ b/rasusa.xml Wed Jul 10 17:01:16 2024 +0000 @@ -1,7 +1,7 @@ <tool id="rasusa" name="rasusa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> <description>Randomly subsample reads to a specified coverage</description> <macros> - <token name="@TOOL_VERSION@">0.8.0</token> + <token name="@TOOL_VERSION@">2.0.0</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@FORMATS@">fastqsanger,fastqsanger.gz,fasta,fasta.gz</token> <xml name="size_units"> @@ -11,35 +11,36 @@ <option value="g">Giga bases</option> <option value="t">Tera bases</option> </xml> - </macros> - <xrefs> - <xref type='bio.tools'>rasusa</xref> - </xrefs> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">rasusa</requirement> - </requirements> - - <command detect_errors="exit_code"><![CDATA[ -rasusa -#if str( $input.input_selector ) == "paired": - #set r1_ext = $input.reads1.extension - #set r2_ext = $input.reads2.extension --i '${input.reads1}' --i '${input.reads2}' --o 'paired_out1.$r1_ext' --o 'paired_out2.$r2_ext' -#elif str( $input.input_selector ) == "paired_collection": - #set r1_ext = $input.collection.forward.extension - #set r2_ext = $input.collection.reverse.extension --i '${input.collection.forward}' --i '${input.collection.reverse}' --o 'paired_out1.$r1_ext' --o 'paired_out2.$r2_ext' -#else: - #set r1_ext = $input.reads.extension --i '${input.reads}' --o 'single_out.$r1_ext' -#end if + <xml name="params_fastq"> + <conditional name="subsample"> + <param name="type" type="select" label="Subsample reads based on"> + <option value="coverage">Coverage</option> + <option value="num_bases">Number of bases</option> + <option value="num_reads">Number of reads</option> + <option value="frac_reads" selected="true">Fraction of reads</option> + </param> + <when value="coverage"> + <param name="genome_size_unit" type="select" label="Specify genome size in"> + <expand macro="size_units" /> + </param> + <param name="genome_size" type="float" min="0" value="" label="Genome size to calculate coverage with respect to"/> + <param argument="--coverage" type="float" min="0" value="" label="The desired coverage to subsample the reads to"/> + </when> + <when value="num_bases"> + <param name="num_bases_unit" type="select" label="Specify number of bases in"> + <expand macro="size_units" /> + </param> + <param name="bases" type="float" min="0" value="" label="Explicitly set the number of bases required"/> + </when> + <when value="num_reads"> + <param argument="--num" type="integer" value="" min="1"/> + </when> + <when value="frac_reads"> + <param argument="--frac" type="float" value="0.1" min="0" max="1"/> + </when> + </conditional> + </xml> + <token name="@FASTQ_SUBSAMPLE_OPTIONS@"><![CDATA[ #if str( $subsample.type ) == "coverage": --genome-size '$subsample.genome_size$subsample.genome_size_unit' --coverage $subsample.coverage @@ -50,68 +51,96 @@ #elif str( $subsample.type ) == "frac_reads": --frac $subsample.frac #end if --s $seed #if $r1_ext.endswith(".gz") or $r2_ext.endswith(".gz") --output-type g +#end if ]]> + </token> + </macros> + <xrefs> + <xref type='bio.tools'>rasusa</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">rasusa</requirement> + <requirement type="package" version="1.20">samtools</requirement> + </requirements> + + <command detect_errors="exit_code"><![CDATA[ +#if str( $input.input_selector ) == "aligned": +ln -s '$bam' 'input.bam' && +ln -s '$bam.metadata.bam_index' 'input.bam.bai' && +rasusa aln +--coverage $input.coverage +--step-size $input.step_size +#else: +rasusa reads #end if -&& + +#if $seed +-s $seed +#end if #if str( $input.input_selector ) == "paired": + #set r1_ext = $input.reads1.extension + #set r2_ext = $input.reads2.extension +-o 'paired_out1.$r1_ext' +-o 'paired_out2.$r2_ext' +@FASTQ_SUBSAMPLE_OPTIONS@ +'${input.reads1}' +'${input.reads2}' && mv 'paired_out1.$r1_ext' '$paired_output1' && mv 'paired_out2.$r2_ext' '$paired_output2' + #elif str( $input.input_selector ) == "paired_collection": + #set r1_ext = $input.collection.forward.extension + #set r2_ext = $input.collection.reverse.extension +-o 'paired_out1.$r1_ext' +-o 'paired_out2.$r2_ext' +@FASTQ_SUBSAMPLE_OPTIONS@ +'${input.collection.forward}' +'${input.collection.reverse}' && mv 'paired_out1.$r1_ext' '${collection_output.forward}' && mv 'paired_out2.$r2_ext' '${collection_output.reverse}' -#else: + +#elif str( $input.input_selector ) == "single": + #set r1_ext = $input.reads.extension +-o 'single_out.$r1_ext' +@FASTQ_SUBSAMPLE_OPTIONS@ +'${input.reads}' && mv 'single_out.$r1_ext' '$single_output' + +#elif str( $input.input_selector ) == "aligned": +'input.bam' | samtools sort --no-PG -@ 1 -T '\${TMPDIR:-.}' -O bam -o '$bam_output' - #end if ]]></command> <inputs> <conditional name="input"> <param name="input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data"> - <option value="paired">Paired</option> - <option value="single">Single</option> - <option value="paired_collection">Paired Collection</option> + <option value="paired">Paired-end FASTQ</option> + <option value="single">Single-end FASTQ</option> + <option value="paired_collection">Paired FASTQ Collection</option> + <option value="aligned">BAM file of aligned reads</option> </param> <when value="paired"> <param name="reads1" type="data" format="@FORMATS@" label="Select first set of reads" help="Specify dataset with forward reads"/> <param name="reads2" type="data" format="@FORMATS@" label="Select second set of reads" help="Specify dataset with reverse reads"/> + <expand macro="params_fastq" /> </when> <when value="single"> <param name="reads" type="data" format="@FORMATS@" label="Select fasta/fastq dataset" help="Specify dataset with single reads"/> + <expand macro="params_fastq" /> </when> <when value="paired_collection"> <param name="collection" format="@FORMATS@" type="data_collection" collection_type="paired" label="Select a paired collection"/> + <expand macro="params_fastq" /> + </when> + <when value="aligned"> + <param name="bam" format="sam,bam" type="data" label="Select BAM file(s) with alignments"/> + <param argument="--coverage" type="integer" min="0" optional="true" value="" label="The desired depth of coverage to subsample the alignment to"/> + <param type="integer" argument="--step-size" value="100" label="When a region has less than the desired coverage, the step size to move along the chromosome to find more reads." + help="The lowest of the step and the minimum end coordinate of the reads in the region will be used. This parameter can have a significant impact on the runtime of the subsampling process."/> </when> </conditional> - <conditional name="subsample"> - <param name="type" type="select" label="Subsample reads based on"> - <option value="coverage">Coverage</option> - <option value="num_bases">Number of bases</option> - <option value="num_reads">Number of reads</option> - <option value="frac_reads" selected="true">Fraction of reads</option> - </param> - <when value="coverage"> - <param name="genome_size_unit" type="select" label="Specify genome size in"> - <expand macro="size_units" /> - </param> - <param name="genome_size" type="float" min="0" value="" label="Genome size to calculate coverage with respect to"/> - <param argument="--coverage" type="float" min="0" value="" label="The desired coverage to sub-sample the reads to"/> - </when> - <when value="num_bases"> - <param name="num_bases_unit" type="select" label="Specify number of bases in"> - <expand macro="size_units" /> - </param> - <param name="bases" type="float" min="0" value="" label="Explicitly set the number of bases required"/> - </when> - <when value="num_reads"> - <param argument="--num" type="integer" value="" min="1"/> - </when> - <when value="frac_reads"> - <param argument="--frac" type="float" value="0.1" min="0" max="1"/> - </when> - </conditional> - <param type="integer" name="seed" optional="true" label="Random seed to use"/> + <param type="integer" argument="--seed" optional="true" label="Random seed to use"/> </inputs> <outputs> <data name="paired_output1" label="${tool.name} on ${on_string}: paired-end r1" format_source="reads1"> @@ -128,6 +157,9 @@ <data name="forward" label="${tool.name} on ${input.collection.forward.name}: paired-end r1" format_source="collection['forward']"/> <data name="reverse" label="${tool.name} on ${input.collection.reverse.name}: paired-end R2" format_source="collection['reverse']"/> </collection> + <data name="bam_output" label="${tool.name} on ${on_string}: BAM" format="bam"> + <filter>input['input_selector'] == 'aligned'</filter> + </data> </outputs> <tests> <test expect_num_outputs="1"> @@ -163,7 +195,7 @@ <output name="paired_output2" value="paired2_by_coverage_k.fastq.gz" ftype="fastqsanger.gz"/> </test> <test expect_num_outputs="3"> - <!-- test 3: paired-collection fastq by coverage in mb--> + <!-- test 3: paired-collection fastq by coverage in mb --> <conditional name="input"> <param name="input_selector" value="paired_collection"/> <param name="collection"> @@ -232,7 +264,7 @@ <output name="paired_output2" value="paired2_by_num_reads.fasta.gz" ftype="fasta.gz"/> </test> <test expect_num_outputs="3"> - <!-- test 7: paired-collection fasta by fraction reads--> + <!-- test 7: paired-collection fasta by fraction reads --> <conditional name="input"> <param name="input_selector" value="paired_collection"/> <param name="collection"> @@ -252,6 +284,16 @@ <element name="reverse" file="paired2_by_frac_reads.fasta" ftype="fasta"/> </output_collection> </test> + <test expect_num_outputs="1"> + <!-- test 8: bam input --> + <conditional name="input"> + <param name="input_selector" value="aligned"/> + <param name="bam" value="input.bam" /> + </conditional> + <param name="coverage" value="1"/> + <param name="seed" value="1"/> + <output name="bam_output" value="output.bam" ftype="bam"/> + </test> </tests> <help><![CDATA[