Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat

comparison rmarkdown_samtools_flagstat.xml @ 4:1723d63c7d95 draft

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update
author mingchen0919
date Fri, 29 Dec 2017 21:22:21 -0500
parents 8354d118baab
children 2a244f3c48a9
comparison
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3:8354d118baab 4:1723d63c7d95
11 <stdio> 11 <stdio>
12 <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/> 12 <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
13 </stdio> 13 </stdio>
14 <command><![CDATA[ Rscript '${__tool_directory__}/rmarkdown_samtools_flagstat_render.R' 14 <command><![CDATA[ Rscript '${__tool_directory__}/rmarkdown_samtools_flagstat_render.R'
15 -e $echo 15 -e $echo
16 -b $input_bam 16 -b '$input_bam'
17 -n $input_bam.name 17 -n '$input_bam.name'
18 -r $report 18 -r $report
19 -d $report.files_path 19 -d $report.files_path
20 -s $sink_message 20 -s $sink_message
21 -t '${__tool_directory__}/rmarkdown_samtools_flagstat.Rmd' 21 -t '${__tool_directory__}/rmarkdown_samtools_flagstat.Rmd'
22 ]]></command> 22 ]]></command>