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comparison samtools_view.xml @ 9:be7c8e8a5d08 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit d15d26f8596e3220fa7aadc76e8623d42b27280d"
author iuc
date Mon, 04 Jan 2021 10:42:59 +0000
parents a8d747577392
children 0b341e4e6ec1
comparison
equal deleted inserted replaced
8:a8d747577392 9:be7c8e8a5d08
1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy2"> 1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy3">
2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> 2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@REF_DATA@"> 5 <token name="@REF_DATA@">
6 ## additional reference data 6 ## additional reference data
41 </expand> 41 </expand>
42 <expand macro="stdio"/> 42 <expand macro="stdio"/>
43 <expand macro="version_command"/> 43 <expand macro="version_command"/>
44 <command><![CDATA[ 44 <command><![CDATA[
45 @ADDTHREADS@ 45 @ADDTHREADS@
46 @ADDMEMORY@
46 ## prepare reference data 47 ## prepare reference data
47 @PREPARE_FASTA_IDX@ 48 @PREPARE_FASTA_IDX@
48 @PREPARE_IDX@ 49 @PREPARE_IDX@
49 50
50 ## determine the output format flag to pass to samtools view 51 ## determine the output format flag to pass to samtools view
222 #if str($mode.output_options.reads_report_type) != 'count': 223 #if str($mode.output_options.reads_report_type) != 'count':
223 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM 224 ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
224 ## then sort the output by coordinate, 225 ## then sort the output by coordinate,
225 #if not $input.is_of_type('bam') and str($mode.output_options.output_format.oformat) == 'bam': 226 #if not $input.is_of_type('bam') and str($mode.output_options.output_format.oformat) == 'bam':
226 && samtools sort 227 && samtools sort
227 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" 228 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
228 -O bam 229 -O bam
229 -o tmpsam 230 -o tmpsam
230 outfile 231 outfile
231 && mv tmpsam outfile 232 && mv tmpsam outfile
232 #if $with_non_selected_reads_output: 233 #if $with_non_selected_reads_output:
233 && samtools sort 234 && samtools sort
234 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" 235 -@ \$addthreads -m \$addmemory"M" -T "\${TMPDIR:-.}"
235 -O bam 236 -O bam
236 -o tmpsam 237 -o tmpsam
237 inv_outfile 238 inv_outfile
238 && mv tmpsam inv_outfile 239 && mv tmpsam inv_outfile
239 #end if 240 #end if