Mercurial > repos > matthias > stacks2_gstacks

comparison stacks_gstacks.xml @ 2:4301ded2ea50 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9c41b2599125298b1a4d9ffb2511cdc87ff79a73
author matthias
date Tue, 18 Dec 2018 12:58:51 -0500
parents 192f1d5f301e
children 285e1f85c11a
comparison
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1:192f1d5f301e 2:4301ded2ea50
8 <command><![CDATA[ 8 <command><![CDATA[
9 @CLEAN_EXT@ 9 @CLEAN_EXT@
10 10
11 mkdir bam_inputs stacks_outputs && 11 mkdir bam_inputs stacks_outputs &&
12 #if $mode_cond.mode_select == "denovo" and not $popmap: 12 #if $mode_cond.mode_select == "denovo" and not $popmap:
13 #if $input_type.input_type_selector == 'manual': 13 ## since collections have no len .. yet
14 #set count = len($input_type.input_bam) 14 #try:
15 #else 15 #set count = len($input_bam)
16 #set count = len($input_type.input_bam.keys()) 16 #except:
17 #end if 17 #set count = len($input_bam.keys())
18 #end try
18 #if count == 1: 19 #if count == 1:
19 #for $bam in $input_bam: 20 #for $bam in $input_bam:
20 ln -s '$bam' bam_inputs/catalog.bam && 21 ln -s '$bam' bam_inputs/catalog.bam &&
21 #end for 22 #end for
22 #else 23 #else
174 </outputs> 175 </outputs>
175 176
176 <tests> 177 <tests>
177 <!-- denovomode, w popmap --> 178 <!-- denovomode, w popmap -->
178 <test> 179 <test>
179 <param name="input_bam"> 180 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
180 <collection type="list">
181 <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
182 <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
183 </collection>
184 </param>
185 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 181 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
186 <conditional name="mode_cond"> 182 <conditional name="mode_cond">
187 <param name="mode_select" value="denovo"/> 183 <param name="mode_select" value="denovo"/>
188 </conditional> 184 </conditional>
189 <param name="add_log" value="yes" /> 185 <param name="add_log" value="yes" />
244 <has_text text="--rm-pcr-duplicates" /> 240 <has_text text="--rm-pcr-duplicates" />
245 </assert_command> 241 </assert_command>
246 </test> 242 </test>
247 <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model --> 243 <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
248 <test> 244 <test>
249 <param name="input_bam"> 245 <param name="input_bam" ftype="bam" value="refmap/PopA_01.bam,refmap/PopA_02.bam"/>
250 <collection type="list">
251 <element name="PopA_01" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
252 <element name="PopA_02" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
253 </collection>
254 </param>
255 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> 246 <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />
256 <conditional name="mode_cond"> 247 <conditional name="mode_cond">
257 <param name="mode_select" value="refbased"/> 248 <param name="mode_select" value="refbased"/>
258 <conditional name="paired_cond"> 249 <conditional name="paired_cond">
259 <param name="paired_select" value="--unpaired"/> 250 <param name="paired_select" value="--unpaired"/>
288 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output> 279 <output name="output_log"><assert_contents><has_text text="gstacks is done." /></assert_contents></output>
289 <output_collection name="gstacks_out" type="list" count="2"/> 280 <output_collection name="gstacks_out" type="list" count="2"/>
290 </test> 281 </test>
291 <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe --> 282 <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe -->
292 <test> 283 <test>
293 <param name="input_bam"> 284 <param name="input_bam" ftype="bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
294 <collection type="list">
295 <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
296 <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
297 </collection>
298 </param>
299 <conditional name="mode_cond"> 285 <conditional name="mode_cond">
300 <param name="mode_select" value="refbased"/> 286 <param name="mode_select" value="refbased"/>
301 <conditional name="paired_cond"> 287 <conditional name="paired_cond">
302 <param name="paired_select" value="--ignore-pe-reads"/> 288 <param name="paired_select" value="--ignore-pe-reads"/>
303 </conditional> 289 </conditional>