Mercurial > repos > iuc > stacks_cstacks
comparison stacks_cstacks.xml @ 12:40cde06ae34a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
author | iuc |
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date | Fri, 07 Apr 2023 22:05:09 +0000 |
parents | be3df81c0353 |
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11:be3df81c0353 | 12:40cde06ae34a |
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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> |