Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat

comparison rmarkdown_samtools_flagstat.xml @ 3:8354d118baab draft

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update
author mingchen0919
date Wed, 27 Dec 2017 23:29:32 -0500
parents 77e8e7bc5b44
children 1723d63c7d95
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2:77e8e7bc5b44 3:8354d118baab
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>
23 <inputs> 23 <inputs>
24 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/> 24 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
25 <param type="data" name="input_bam" label="BAM file" optional="False"/> 25 <param type="data" format="bam,sam" name="input_bam" label="BAM/SAM file" optional="False"/>
26 </inputs> 26 </inputs>
27 <outputs> 27 <outputs>
28 <data name="report" format="html" label="tool name report" hidden="false"/> 28 <data name="report" format="html" label="tool name report" hidden="false"/>
29 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/> 29 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
30 </outputs> 30 </outputs>
31 <help><![CDATA[<code>samtools flagstat in.sam|in.bam|in.cram</code> 31 <help><![CDATA[
32 samtools flagstat in.sam|in.bam|in.cram
32 33
33 Does a full pass through the input file to calculate and print statistics to stdout]]></help> 34 Does a full pass through the input file to calculate and print statistics to stdout]]></help>
34 <citations> 35 <citations>
35 <citation><![CDATA[ 36 <citation type="bibtex"><![CDATA[
36 @article{allaire2016rmarkdown, 37 @article{allaire2016rmarkdown,
37 title={rmarkdown: Dynamic Documents for R, 2016}, 38 title={rmarkdown: Dynamic Documents for R, 2016},
38 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff 39 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
39 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, 40 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
40 journal={R package version 0.9}, 41 journal={R package version 0.9},