Mercurial > repos > iuc > stacks_genotypes

comparison macros.xml @ 8:8dc6a3afbe83 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
author iuc
date Thu, 27 Apr 2017 04:19:10 -0400
parents 639f2db87df0
children 5af94af9ec8f
comparison
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7:639f2db87df0 8:8dc6a3afbe83
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.42">stacks</requirement> 5 <requirement type="package" version="1.46">stacks</requirement>
6 <requirement type="package" version="1.2.10">velvet</requirement> 6 <requirement type="package" version="1.2.10">velvet</requirement>
7 <container type="docker">quay.io/biocontainers/stacks:1.42--2</container> 7 <requirement type="package" version="1.1">stacks_summary</requirement>
8 <yield/> 8 <yield/>
9 </requirements> 9 </requirements>
10 </xml> 10 </xml>
11 11
12 <token name="@WRAPPER_VERSION@">1.42</token> 12 <token name="@WRAPPER_VERSION@">1.46</token>
13 13
14 <xml name="stdio"> 14 <xml name="stdio">
15 <stdio> 15 <stdio>
16 <exit_code range="1:" level="fatal" description="Error in Stacks execution" /> 16 <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
17 </stdio> 17 </stdio>
88 <option value="xhoI">xhoI</option> 88 <option value="xhoI">xhoI</option>
89 <option value="csp6I">csp6I</option> 89 <option value="csp6I">csp6I</option>
90 <option value="bsaHI">bsaHI</option> 90 <option value="bsaHI">bsaHI</option>
91 <option value="hpaII">hpaII</option> 91 <option value="hpaII">hpaII</option>
92 <option value="ncoI">ncoI</option> 92 <option value="ncoI">ncoI</option>
93 <option value="ApaLI">ApaLI</option>
93 </xml> 94 </xml>
94 95
95 <xml name="cross_types"> 96 <xml name="cross_types">
96 <option value="CP">CP (F1 cross)</option> 97 <option value="CP">CP (F1 cross)</option>
97 <option value="F2">F2 (F2 cross)</option> 98 <option value="F2">F2 (F2 cross)</option>
98 <option value="BC1">BC1 (backcross)</option> 99 <option value="BC1">BC1 (backcross)</option>
99 <option value="DH">DH (double haploid cross)</option> 100 <option value="DH">DH (double haploid cross)</option>
100 <option value="GEN">GEN (generic, unspecific to any map type)</option> 101 <option value="GEN">GEN (generic, unspecific to any map type)</option>
101 </xml> 102 </xml>
103
104 <token name="@CLEAN_EXT@">
105 <![CDATA[
106 #from os.path import splitext
107 #import re
108 #def clean_ext($identifier)
109 #while $identifier.endswith(('.1', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam'))
110 #set $identifier = splitext($identifier)[0]
111 #end while
112 $identifier#slurp
113 #end def
114 ]]>
115 </token>
102 116
103 <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@"> 117 <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@">
104 <![CDATA[ 118 <![CDATA[
105 ## We need to do this as the output file names contains the value of an option (min progeny) 119 ## We need to do this as the output file names contains the value of an option (min progeny)
106 && 120 &&