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comparison rmarkdown_samtools_flagstat.xml @ 8:b6ad018c5fa6 draft default tip

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author mingchen0919
date Sun, 31 Dec 2017 16:03:34 -0500
parents 83d7158672a7
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7:83d7158672a7 8:b6ad018c5fa6
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" format="bam,sam" name="input_bam" label="BAM/SAM 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="rmarkdown flagstat 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[ 31 <help><![CDATA[
32 samtools flagstat in.sam|in.bam|in.cram 32 samtools flagstat in.sam|in.bam|in.cram
33 33
39 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
40 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, 40 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
41 journal={R package version 0.9}, 41 journal={R package version 0.9},
42 volume={6}, 42 volume={6},
43 year={2016} 43 year={2016}
44 ]]></citation> 44 }]]></citation>
45 <citation type="bibtex"><![CDATA[@article{li2009sequence, 45 <citation type="bibtex"><![CDATA[@article{li2009sequence,
46 title={The sequence alignment/map format and SAMtools}, 46 title={The sequence alignment/map format and SAMtools},
47 author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard}, 47 author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard},
48 journal={Bioinformatics}, 48 journal={Bioinformatics},
49 volume={25}, 49 volume={25},