Mercurial > repos > devteam > bwa

comparison bwa.xml @ 12:bd3a1e0de84c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 13b3ab10ff1a2e4be39b44f885df6bbe7c23099a
author devteam
date Fri, 30 Dec 2016 08:11:12 -0500
parents 546ada4a9f43
children 53646aaaafef
comparison
equal deleted inserted replaced
11:546ada4a9f43 12:bd3a1e0de84c
216 @read_group_options@ 216 @read_group_options@
217 217
218 "${reference_fasta_filename}" first.sai "${input_type.bam_input}" 218 "${reference_fasta_filename}" first.sai "${input_type.bam_input}"
219 #end if 219 #end if
220 220
221 | samtools view -Sb - > temporary_bam_file.bam && 221 | samtools sort -O bam -o '$bam_output'
222
223 samtools sort -f temporary_bam_file.bam ${bam_output}
224 ]]> 222 ]]>
225 </command> 223 </command>
226 224
227 <inputs> 225 <inputs>
228 <expand macro="reference_source_conditional" /> 226 <expand macro="reference_source_conditional" />