Mercurial > repos > iuc > stacks2_denovomap

comparison stacks_denovomap.xml @ 5:04db7fd6b238 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"
author iuc
date Thu, 14 Apr 2022 09:20:20 +0000
parents ad5ab22ffe24
children 89eb29319bf4
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4:405a212b32ab 5:04db7fd6b238
1 <tool id="stacks2_denovomap" name="Stacks2: de novo map" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> 1 <tool id="stacks2_denovomap" name="Stacks2: de novo map" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description> 2 <description>the Stacks pipeline without a reference genome (denovo_map.pl)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
40 ## need to gzip it again for downstream calls like populations) 40 ## need to gzip it again for downstream calls like populations)
41 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf 41 && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf
42 ]]></command> 42 ]]></command>
43 43
44 <inputs> 44 <inputs>
45 <expand macro="fastq_input"/> 45 <expand macro="fastq_input" multiple="true" listtype="list:paired"/>
46 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map"/> 46 <param argument="--popmap" type="data" optional="true" format="tabular,txt" label="Population map"/>
47 <section name="assembly_options" title="Assembly options" expanded="true"> 47 <section name="assembly_options" title="Assembly options" expanded="true">
48 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual" help="used in ustacks"/> 48 <param name="M" argument="-M" type="integer" value="2" label="Number of mismatches allowed between loci when processing a single individual" help="used in ustacks"/>
49 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog" help="used in cstacks; suggested: set to -M"/> 49 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between loci when building the catalog" help="used in cstacks; suggested: set to -M"/>
50 </section> 50 </section>