Mercurial > repos > devteam > bowtie2
comparison bowtie2_wrapper.xml @ 26:09b2cdb7ace5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 41371d219eaafc811eadf7646a7f0ecf002e4239"
author | iuc |
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date | Tue, 12 Jan 2021 16:58:26 +0000 |
parents | 749c918495f7 |
children | a6d65b0c67af |
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25:749c918495f7 | 26:09b2cdb7ace5 |
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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 |