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comparison samtools_view.xml @ 5:f2b321f691e4 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e2a10eeee8765ba6cf03847562e56cdaeaf4ba5c"
author iuc
date Thu, 05 Sep 2019 19:33:58 -0400
parents 097c44aaf6d4
children 1e7eb419a5be
comparison
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4:2ec9fb20bb27 5:f2b321f691e4
118 118
119 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM 119 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
120 ## then sort the output by coordinate, 120 ## then sort the output by coordinate,
121 #if not $input.is_of_type('bam') and $outtype == 'bam': 121 #if not $input.is_of_type('bam') and $outtype == 'bam':
122 && samtools sort 122 && samtools sort
123 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp 123 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
124 -O bam 124 -O bam
125 -o 'tmpsam' 125 -o 'tmpsam'
126 outfile 126 outfile
127 && mv tmpsam outfile 127 && mv tmpsam outfile
128 #if $adv_output.outputpassing == 'yes': 128 #if $adv_output.outputpassing == 'yes':
129 && samtools sort 129 && samtools sort
130 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp 130 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
131 -O bam 131 -O bam
132 -o 'tmpsam' 132 -o 'tmpsam'
133 inv_outfile 133 inv_outfile
134 && mv tmpsam inv_outfile 134 && mv tmpsam inv_outfile
135 #end if 135 #end if