Mercurial > repos > iuc > vg_deconstruct
diff deconstruct.xml @ 0:a347dad1f305 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
author | iuc |
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date | Thu, 09 Apr 2020 04:36:41 -0400 |
parents | |
children | 76d18b1e970b |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deconstruct.xml Thu Apr 09 04:36:41 2020 -0400 @@ -0,0 +1,82 @@ +<tool id="vg_deconstruct" name="vg deconstruct" version="@TOOL_VERSION@"> + <description>construct a dynamic succinct variation graph</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +ln -s '$infile' ./infile.${infile.ext} && + +vg deconstruct +#if $path: + --path '${','.join([$p for $p in $path])}' +#end if +#if $path_prefix + --path-prefix '${','.join([$p for $p in $path_prefix])}' +#end if +#if $alt_prefix + --alt-prefix '${','.join([$p for $p in $alt_prefix])}' +#end if +#if $snarls: + --snarls '$snarls' +#end if +$path_traversals ## -e +--threads=\${GALAXY_SLOTS:-1} +./infile.${infile.ext} + +> '$output' + + ]]></command> + <inputs> + <param name="infile" type="data" format="xg,odgi" label="Graph files" /> + <param argument="--path" type="text" value="" label="A reference path to deconstruct against" + help="comma-separated list accepted"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param argument="--path-prefix" type="text" value="" label="All paths beginning with this value used as reference" + help="comma-separated list accepted"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param argument="--alt-prefix" type="text" value="" label="Non-reference paths beginning with with this value get lumped together to same sample in VCF" + help="comma-separated list accepted"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + </sanitizer> + </param> + <param argument="--snarls" type="data" format="xg,odgi" label="Snarls files" optional="true" + help="from `vg snarls` to avoid recomputing" /> + + <param argument="--path-traversals" type="boolean" truevalue="--path-traversals" falsevalue="" checked="false" + label="Only consider traversals that correspond to paths in the grpah" /> + </inputs> + <outputs> + <data name="output" format="vcf" /> + </outputs> + <tests> + <test> + <param name="infile" value="hla.xg" /> + <param name="path" value="gi|568815592:29791752-29792749" /> + <param name="path_traversals" value="true" /> + <output name="output" file="hla_variants.vcf" /> + </test> + </tests> + <help><![CDATA[ +variation graph (vg) deconstruct module +----------------------------------- + +Creates VCF records for Snarls present in a graph (relative to a chosen reference path). + + ]]></help> + <expand macro="citations"> + </expand> +</tool>