Mercurial > repos > iuc > samtools_coverage
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit 4d0362c336f67d05086298ab4980c1d922d71c6e"
author | iuc |
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date | Tue, 28 Sep 2021 15:10:16 +0000 |
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children | ae36fab06bc2 |
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<tool id="samtools_coverage" name="Samtools coverage" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>computes the depth at each position or region</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @PREPARE_IDX@ samtools coverage #if $condition_input.input_pooling == "Yes": ${ ' '.join( [ "'%s'" % $x for $x in $condition_input.input] ) } #else '$condition_input.input' #end if -l $additional_options.min_read_length -q $additional_options.min_mq -Q $additional_options.min_bq #set $filter = $additional_options.required_flags @FLAGS@ -rf $flags #set $filter = $additional_options.skipped_flags @FLAGS@ -ff $flags #if $condition_histogram.histogram_select == "yes" -m -w $condition_histogram.n_bins #if $condition_histogram.region != "": -r '$condition_histogram.region' #end if #end if -o '$output' ]]></command> <inputs> <conditional name="condition_input"> <param name="input_pooling" type="select" label="Are you pooling bam files?" help="Calculate the coverage for multiple bam files" > <option value="No" selected="True">No</option> <option value="Yes">Yes</option> </param> <when value="No" > <param name="input" type="data" format="bam" multiple="true" label="BAM file"/> </when> <when value="Yes"> <param name="input" type="data" format="bam" multiple="true" label="BAM files to be pooled"/> </when> </conditional> <section name="additional_options" title="Additional Options" expanded="true"> <param name="min_read_length" argument="-l" type="integer" min="0" value="0" label="Minimum read length" help="Ignore reads shorter than INT base pairs (Default = 0)" /> <param name="min_mq" argument="-q" type="integer" min="0" value="0" label="Minimum mapping quality" help="Minimum mapping quality for an alignment to be used (Default = 0)" /> <param name="min_bq" argument="-Q" type="integer" min="0" value="0" label="Minimum base quality" help="Minimum base quality for a base to be considered (Default = 0)" /> <param name="required_flags" argument="--rf" type="select" multiple="True" label="Require that these flags are set"> <expand macro="flag_options" /> </param> <param name="skipped_flags" argument="--ff" type="select" multiple="True" label="Exclude reads with any of the following flags set"> <expand macro="flag_options" s4="true" s256="true" s512="true" s1024="true"/> </param> </section> <conditional name="condition_histogram"> <param name="histogram_select" argument="-m" type="select" label="Histogram" help="Show histogram instead of tabular output"> <option value="no" selected="true">No</option> <option value="yes">Yes</option> </param> <when value="yes"> <param name="n_bins" argument="-w" type="integer" min="1" value="100" label="Number of bins in histogram" help="Number of bins in histogram" /> <param name="region" argument="-r" type="text" value="" label="Show specified region" help="Show specified region. Format: chr:start-end." /> </when> <when value="no" /> </conditional> </inputs> <outputs> <data name="output" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}" /> </outputs> <tests> <test> <param name="input" value="test_1.bam" ftype="bam" /> <output name="output" file="results_1.tabular" ftype="tabular" /> </test> <test> <param name="input" value="test_1.bam" ftype="bam" /> <param name="histogram_select" value="yes" /> <param name="n_bins" value="50" /> <output name="output" file="results_2.txt" ftype="tabular" /> </test> <test> <param name="input_pooling" value="Yes" /> <param name="input" value="test_1.bam,test_2.bam" ftype="bam" /> <param name="histogram_select" value="yes" /> <param name="n_bins" value="100" /> <output name="output" file="results_3.txt" ftype="tabular" /> </test> </tests> <help><![CDATA[ **What it does** This tool runs the ``samtools coverage`` command. Computes the depth at each position or region and draws an ASCII-art histogram or tabulated text. If you select to pool the bam files, then it calculates coverage for the combined files. The tabulated form uses the following headings: - rname Reference name / chromosome - startpos Start position - endpos End position (or sequence length) - numreads Number reads aligned to the region (after filtering) - covbases Number of covered bases with depth >= 1 - coverage Proportion of covered bases [0..1] - meandepth Mean depth of coverage - meanbaseq Mean baseQ in covered region - meanmapq Mean mapQ of selected reads ]]></help> <expand macro="citations"/> </tool>