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comparison bowtie2_wrapper.xml @ 26:1fc8d53bc352 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:35:26 -0400
parents 739b008acace
children c9105910063f
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25:739b008acace 26:1fc8d53bc352
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} -O bam -o '$output' 308 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
309 #else if $sam_options.reorder: 309 #else if $sam_options.reorder:
310 | samtools view -bS - -o '$output' 310 | samtools view -bS - -o '$output'
311 #else: 311 #else:
312 > '$output' 312 > '$output'
313 #end if 313 #end if