Mercurial > repos > matthias > stacks2_tsv2bam

comparison macros.xml @ 1:9cd90b2f08f7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
author matthias
date Fri, 30 Nov 2018 07:36:41 -0500
parents 99d0b19ef534
children c3a4fb832c18
comparison
equal deleted inserted replaced
0:99d0b19ef534 1:9cd90b2f08f7
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="@WRAPPER_VERSION@">stacks</requirement> 5 <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
6 <yield/> 6 <yield/>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9 9
10 <token name="@WRAPPER_VERSION@">2.2=he860b03_0</token> 10 <token name="@STACKS_VERSION@">2.2</token>
11 <token name="@WRAPPER_VERSION@">1</token>
11 12
12 <xml name="stdio"> 13 <xml name="stdio">
13 <stdio> 14 <stdio>
14 <exit_code range="1:" level="fatal" description="Error in Stacks execution" /> 15 <exit_code range="1:" level="fatal" description="Error in Stacks execution" />
15 </stdio> 16 </stdio>
172 ln -s '$sample' '${data_path}' && 173 ln -s '$sample' '${data_path}' &&
173 ]]></token> 174 ]]></token>
174 175
175 <!-- macro and token for BAM input--> 176 <!-- macro and token for BAM input-->
176 <xml name="bam_input_macro"> 177 <xml name="bam_input_macro">
177 <conditional name="input_type"> 178 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
178 <param name="input_type_selector" type="select" label="BAM files">
179 <option value="list">data set list</option>
180 <option value="manual">data sets</option>
181 </param>
182 <when value="manual">
183 <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
184 </when>
185 <when value="list">
186 <param name="input_bam" format="bam" type="data_collection" collection_type="list" label="BAM files" />
187 </when>
188 </conditional>
189 </xml> 179 </xml>
190 <token name="@BAM_INPUT@"><![CDATA[ 180 <token name="@BAM_INPUT@"><![CDATA[
191 #set $bamlist = "" 181 #set $bamlist = ""
192 #for $bam in $input_type.input_bam: 182 #for $bam in $input_bam:
193 #set $filename = $clean_ext($bam.element_identifier)+".bam" 183 #set $filename = $clean_ext($bam.element_identifier)+".bam"
194 #if re.search('.*\.bam$', $filename) 184 #if re.search('.*\.bam$', $filename)
195 ln -s '$bam' bam_inputs/$filename && 185 ln -s '$bam' bam_inputs/$filename &&
196 #set bamlist += " -B 'bam_inputs/"+$filename+"'" 186 #set bamlist += " -B 'bam_inputs/"+$filename+"'"
197 #end if 187 #end if