Mercurial > repos > iuc > cnvkit_access
view access.xml @ 0:22878d2aff05 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
author | iuc |
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date | Sun, 14 May 2023 20:09:17 +0000 |
parents | |
children | 9f18bcf53f92 |
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<tool id="cnvkit_access" name="CNVkit Access" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>Calculate the sequence-accessible coordinates in chromosomes</description> <macros> <import>macros.xml</import> </macros> <expand macro="xrefs"/> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #import re ln -s '$fa_fname' ./genome.fasta && #if $exclude #set $names = [] #set $x=1 #for $x, $exc in enumerate($exclude): #set $name_base = re.sub('[^\w\-_\.]', '_', $exc.element_identifier) #set $name = $name_base + '_' + str(x) #silent $names.append( $name ) ln -s '$exc' ${name}.bed && #end for #end if cnvkit.py access ./genome.fasta #if $exclude #for $name in $names: --exclude ${name}.bed #end for #end if #if str($min_gap_size) --min-gap-size $min_gap_size #end if --output access-excludes.bed ]]></command> <inputs> <param name="fa_fname" type="data" format="fasta" label="Target coverage file" help="Reference genome fasta file" /> <param argument="--min-gap-size" optional="true" type="integer" label="Minimum gap size between accessible sequence regions" min="0" value="5000" help="Regions separated by less than this distance will be joined together" /> <param argument="--exclude" type="data" optional="true" format="bed" multiple="true" label="Additional regions to exclude" help="" /> </inputs> <outputs> <data name="out_sample_access" format="bed" label="${tool.name} on ${on_string}: Sequence-accessible coordinates" from_work_dir="access-excludes.bed" /> </outputs> <tests> <test expect_num_outputs="1"> <param name="fa_fname" ftype="fasta" value="genome.fasta" /> <param name="min_gap_size" value="2500" /> <param name="exclude" ftype="bed" value="excludes.bed" /> <output name="out_sample_access" file="access-excludes.bed" /> </test> <test expect_num_outputs="1"> <param name="fa_fname" ftype="fasta" value="genome.fasta" /> <param name="min_gap_size" value="2500" /> <param name="exclude" ftype="bed" value="excludes.bed,excludes_1.bed" /> <output name="out_sample_access" file="access-excludes.bed" /> </test> </tests> <help><![CDATA[ The access command computes the locations of the accessible sequence regions for a given reference genome based on these masked-out sequences, treating long spans of āNā characters as the inaccessible regions and outputting the coordinates of the regions between them. ]]></help> <expand macro="citations" /> </tool>