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comparison bowtie2_wrapper.xml @ 27:a6d65b0c67af draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit d142d9cd5a8db8a87184c4b7622ea8de8355894f"
author iuc
date Sat, 10 Jul 2021 07:45:14 +0000
parents 09b2cdb7ace5
children cd659e8cc5fa
comparison
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26:09b2cdb7ace5 27:a6d65b0c67af
1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="18.01"> 1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05">
2 <description>- map reads against reference genome</description> 2 <description>- map reads against reference genome</description>
3 <macros> 3 <macros>
4 <import>bowtie2_macros.xml</import> 4 <import>bowtie2_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
303 2> '$mapping_stats' 303 2> '$mapping_stats'
304 #end if 304 #end if
305 305
306 ## output file 306 ## output file
307 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''): 307 #if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
308 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output' 308 | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
309 #else if $sam_options.reorder: 309 #else if $sam_options.reorder:
310 | samtools view -bS - -o '$output' 310 | samtools view --no-PG -bS - -o '$output'
311 #else: 311 #else:
312 > '$output' 312 > '$output'
313 #end if 313 #end if
314 314
315 ## rename unaligned sequence files 315 ## rename unaligned sequence files