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comparison bwa.xml @ 12:086ba7b646e5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:35:56 -0400
parents 6def3ba376a7
children 22b497739c9c
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11:6def3ba376a7 12:086ba7b646e5
207 #end if 207 #end if
208 @read_group_options@ 208 @read_group_options@
209 '${reference_fasta_filename}' first.sai '${input_type.bam_input}' 209 '${reference_fasta_filename}' first.sai '${input_type.bam_input}'
210 #end if 210 #end if
211 211
212 | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '$bam_output' 212 | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$bam_output'
213 ]]> 213 ]]>
214 </command> 214 </command>
215 215
216 <inputs> 216 <inputs>
217 <expand macro="reference_source_conditional"/> 217 <expand macro="reference_source_conditional"/>