Mercurial > repos > iuc > stacks_sstacks

comparison stacks_sstacks.xml @ 9:ecec9bdfc46a 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 21:59:23 +0000
parents 45cc649c9f8a
children
comparison
equal deleted inserted replaced
8:45cc649c9f8a 9:ecec9bdfc46a
1 <tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.0"> 1 <tool id="stacks_sstacks" name="Stacks: sstacks" version="@WRAPPER_VERSION@.1">
2 <description>match stacks to a catalog</description> 2 <description>match stacks to a catalog</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
33 #set $filename = str($input_file.element_identifier) 33 #set $filename = str($input_file.element_identifier)
34 #if not filename.endswith('.tsv') 34 #if not filename.endswith('.tsv')
35 #set $filename = $filename + ".tsv" 35 #set $filename = $filename + ".tsv"
36 #end if 36 #end if
37 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename) 37 #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename)
38 ln -s '${input_file}' 'stacks_inputs/$filename' && 38 ## When using a popmap, stacks write to the input dir (see also below)
39 #if $popmap
40 cp '${input_file}' 'stacks_inputs/$filename' &&
41 #else
42 ln -s '${input_file}' 'stacks_inputs/$filename' &&
43 #end if
39 44
40 #if $filename.endswith('.tags.tsv') 45 #if $filename.endswith('.tags.tsv')
41 #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'" 46 #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'"
42 #end if 47 #end if
43 #end if 48 #end if
80 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" /> 85 <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />
81 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" /> 86 <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" />
82 87
83 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" /> 88 <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" />
84 89
85 <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" /> 90 <param argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />
86 91
87 <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" /> 92 <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" />
88 93
89 <param name="gapped" argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" /> 94 <param argument="--gapped" type="boolean" checked="false" truevalue="--gapped" falsevalue="" label="Perform gapped alignments between stacks" />
90 </inputs> 95 </inputs>
91 96
92 <outputs> 97 <outputs>
93 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" /> 98 <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" />
94 99