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comparison bowtie2_wrapper.xml @ 26:09b2cdb7ace5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
author iuc
date Tue, 12 Jan 2021 16:58:26 +0000
parents 749c918495f7
children a6d65b0c67af
comparison
equal deleted inserted replaced
25:749c918495f7 26:09b2cdb7ace5
1 <tool id="bowtie2" name="Bowtie2" version="2.3.4.3+galaxy0" profile="18.01"> 1 <tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="18.01">
2 <description>- map reads against reference genome</description> 2 <description>- map reads against reference genome</description>
3 <macros> 3 <macros>
4 <import>bowtie2_macros.xml</import> 4 <import>bowtie2_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="2.3.4.1">bowtie2</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
8 <requirement type="package" version="1.9">samtools</requirement> 8 <requirement type="package" version="1.11">samtools</requirement>
9 </requirements> 9 </requirements>
10 <version_command>bowtie2 --version</version_command> 10 <version_command>bowtie2 --version</version_command>
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 ## Use pipefail if available to quit with first non-zero exit code 12 ## Use pipefail if available to quit with first non-zero exit code
13 set -o | grep -q pipefail && set -o pipefail; 13 set -o | grep -q pipefail && set -o pipefail;
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