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comparison rmarkdown_samtools_flagstat.xml @ 2:77e8e7bc5b44 draft

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author mingchen0919
date Wed, 27 Dec 2017 15:19:43 -0500
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1 <tool id="rmarkdown_samtools_flagstat" name="R Markdown samtools flagstat" version="1.0.0">
2 <requirements>
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
4 <requirement type="package" version="1.20.0">r-getopt</requirement>
5 <requirement type="package" version="1.3">r-rmarkdown</requirement>
6 <requirement type="package" version="0.3.5">r-htmltools</requirement>
7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
8 <requirement type="package" version="1.4.1">samtools</requirement>
9 </requirements>
10 <description>simple stats on BAM file</description>
11 <stdio>
12 <regex source="stderr" match="XXX" level="warning" description="Check the warnings_and_errors.txt file for more details."/>
13 </stdio>
14 <command><![CDATA[ Rscript '${__tool_directory__}/rmarkdown_samtools_flagstat_render.R'
15 -e $echo
16 -b $input_bam
17 -n $input_bam.name
18 -r $report
19 -d $report.files_path
20 -s $sink_message
21 -t '${__tool_directory__}/rmarkdown_samtools_flagstat.Rmd'
22 ]]></command>
23 <inputs>
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"/>
26 </inputs>
27 <outputs>
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"/>
30 </outputs>
31 <help><![CDATA[<code>samtools flagstat in.sam|in.bam|in.cram</code>
32
33 Does a full pass through the input file to calculate and print statistics to stdout]]></help>
34 <citations>
35 <citation><![CDATA[
36 @article{allaire2016rmarkdown,
37 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 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
40 journal={R package version 0.9},
41 volume={6},
42 year={2016}
43 ]]></citation>
44 <citation type="bibtex"><![CDATA[@article{li2009sequence,
45 title={The sequence alignment/map format and SAMtools},
46 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 journal={Bioinformatics},
48 volume={25},
49 number={16},
50 pages={2078--2079},
51 year={2009},
52 publisher={Oxford University Press}
53 }]]></citation>
54 </citations>
55 </tool>