Mercurial > repos > iuc > stacks_cstacks

comparison stacks_cstacks.xml @ 9:569caf3bc7aa draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author iuc
date Fri, 07 Apr 2023 21:58:49 +0000
parents 02e57ebafa9c
children
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8:02e57ebafa9c 9:569caf3bc7aa
1 <tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_cstacks" name="Stacks: cstacks" version="@WRAPPER_VERSION@.0">
2 <description>build a catalogue of loci</description> 2 <description>build a catalogue of loci</description>
3 <expand macro="bio_tools"/>
4 <macros> 3 <macros>
5 <import>macros.xml</import> 4 <import>macros.xml</import>
6 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/> 8 <expand macro="stdio"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 #import re 10 #import re
11 11
69 <inputs> 69 <inputs>
70 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" /> 70 <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" />
71 71
72 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" /> 72 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" />
73 73
74 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" /> 74 <param argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
75 75
76 <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/> 76 <param argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/>
77 77
78 <param name="include_multiple" argument="-m" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Include tags in the catalog that match to more than one entry" /> 78 <param name="include_multiple" argument="-m" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Include tags in the catalog that match to more than one entry" />
79 79
80 <conditional name="gapped"> 80 <conditional name="gapped">
81 <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks"> 81 <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks">
82 <option value="no" selected="true">No</option> 82 <option value="no" selected="true">No</option>
83 <option value="yes">Yes</option> 83 <option value="yes">Yes</option>
84 </param> 84 </param>
85 <when value="no"/> 85 <when value="no"/>
86 <when value="yes"> 86 <when value="yes">
87 <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/> 87 <param argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>
88 <param name="min_aln_len" argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/> 88 <param argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>
89 </when> 89 </when>
90 </conditional> 90 </conditional>
91 </inputs> 91 </inputs>
92 92
93 <outputs> 93 <outputs>