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comparison bismark_bowtie2_wrapper.xml @ 3:91f07ff056ca draft

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Uploaded
author bgruening
date Mon, 14 Apr 2014 16:43:14 -0400
parents 82814a8a2395
children 243e8f9fb75b
comparison
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2:82814a8a2395 3:91f07ff056ca
1 <tool id="bismark_bowtie2" name="Bismark" version="0.7.12.1"> 1 <tool id="bismark_bowtie2" name="Bismark" version="0.10.1">
2 <!-- Wrapper compatible with Bismark version 0.7.11 --> 2 <!-- Wrapper compatible with Bismark version 0.10 -->
3 <description>bisulfite mapper (bowtie2)</description> 3 <description>bisulfite mapper (bowtie2)</description>
4 <!--<version_command>bismark version</version_command>--> 4 <!--<version_command>bismark version</version_command>-->
5 <requirements> 5 <requirements>
6 <requirement type="set_environment">SCRIPT_PATH</requirement> 6 <requirement type="set_environment">SCRIPT_PATH</requirement>
7 <requirement type="package" version="0.1.19">samtools</requirement> 7 <requirement type="package" version="0.1.19">samtools</requirement>
10 <parallelism method="basic"></parallelism> 10 <parallelism method="basic"></parallelism>
11 <command interpreter="python"> 11 <command interpreter="python">
12 bismark_wrapper.py 12 bismark_wrapper.py
13 13
14 ## Change this to accommodate the number of threads you have available. 14 ## Change this to accommodate the number of threads you have available.
15 --num-threads 24 15 --num-threads "\${GALAXY_SLOTS:-24}"
16 16
17 --bismark_path \$SCRIPT_PATH 17 --bismark_path \$SCRIPT_PATH
18 18
19 --bowtie2 19 --bowtie2
20 20
69 69
70 -I $singlePaired.minInsert 70 -I $singlePaired.minInsert
71 -X $singlePaired.maxInsert 71 -X $singlePaired.maxInsert
72 #end if 72 #end if
73 73
74 #if $sort_bam:
75 --sort-bam
76 #end if
74 77
75 ## for now hardcode the value for the required memory per thread in --best mode 78 ## for now hardcode the value for the required memory per thread in --best mode
76 --chunkmbs 512 79 --chunkmbs 512
77 80
78 81
174 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" /> 177 <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
175 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" /> 178 <param name="maxInsert" type="integer" value="500" label="Maximum insert size for valid paired-end alignments" />
176 </when> 179 </when>
177 </conditional> 180 </conditional>
178 181
182 <param name="sort_bam" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sort BAM file by chromosomal position (not compatibile with methylation extractor)"/>
179 183
180 <conditional name="params"> 184 <conditional name="params">
181 <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters."> 185 <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
182 <option value="default">Use Defaults</option> 186 <option value="default">Use Defaults</option>
183 <option value="custom">Full parameter list</option> 187 <option value="custom">Full parameter list</option>
340 </action> 344 </action>
341 </when> 345 </when>
342 </conditional> 346 </conditional>
343 </actions> 347 </actions>
344 </data> 348 </data>
345
346
347 </outputs> 349 </outputs>
348 350
349 <tests> 351 <tests>
350 </tests> 352 </tests>
351 353