Mercurial > repos > iuc > stacks2_ustacks

comparison stacks_ustacks.xml @ 5:6df4c5bf0a91 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 09:15:59 +0000
parents 1dce9f3949c9
children cee1b75beeaf
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equal deleted inserted replaced
4:ee07da8dc52d 5:6df4c5bf0a91
1 <tool id="stacks2_ustacks" name="Stacks2: ustacks" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@"> 1 <tool id="stacks2_ustacks" name="Stacks2: ustacks" profile="@PROFILE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Identify unique stacks</description> 2 <description>Identify unique stacks</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"/>
68 && gunzip stacks_outputs/*.gz 68 && gunzip stacks_outputs/*.gz
69 #end if 69 #end if
70 ]]></command> 70 ]]></command>
71 71
72 <inputs> 72 <inputs>
73 <expand macro="fastq_input" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"/> 73 <expand macro="fastq_input" multiple="true" listtype="list:paired" help="Single end data or forward reads. If a paired list is provided only the forward reads are used in ustacks"/>
74 74
75 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/> 75 <param argument="-m" type="integer" value="3" label="Minimum depth of coverage required to create a stack"/>
76 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/> 76 <param argument="-M" type="integer" value="2" label="Maximum distance (in nucleotides) allowed between stacks"/>
77 <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/> 77 <param argument="-N" type="integer" value="" optional="true" label="Maximum distance allowed to align secondary reads to primary stacks" help="(default: M + 2)"/>
78 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads"/> 78 <param argument="-R" type="boolean" checked="false" truevalue="-R" falsevalue="" label="Retain unused reads"/>