Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat

comparison rmarkdown_flagstat.xml @ 0:ba913054bbff draft

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author mingchen0919
date Tue, 26 Dec 2017 19:27:41 -0500
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1 <tool id="rmarkdown_flagstat" name="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>Descriptive stats for BAM dataset</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[
15 Rscript '${__tool_directory__}/tool_template_render.R'
16 -e $echo
17 -r $report
18 -d $report.files_path
19 -s $sink_message
20 -t '${__tool_directory__}/tool_template.Rmd
21 ]]></command>
22 <inputs>
23 <param type="integer" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
24 <param type="data" name="input_bam" label="BAM file" optional="False" format="bam"/>
25 </inputs>
26 <outputs>
27 <data name="report" format="html" label="tool name report" hidden="false"/>
28 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
29 </outputs>
30 <help><![CDATA[Provides counts for each of 13 categories based primarily on bit flags in the FLAG field. Each category in the output is broken down into QC pass and QC fail, which is presented as "#PASS + #FAIL" followed by a description of the category.]]></help>
31 <citations>
32 <citation><![CDATA[
33 @article{allaire2016rmarkdown,
34 title={rmarkdown: Dynamic Documents for R, 2016},
35 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
36 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
37 journal={R package version 0.9},
38 volume={6},
39 year={2016}
40 ]]></citation>
41 <citation type="bibtex"><![CDATA[
42 @article{li2009sequence,
43 title={The sequence alignment/map format and SAMtools},
44 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},
45 journal={Bioinformatics},
46 volume={25},
47 number={16},
48 pages={2078--2079},
49 year={2009},
50 publisher={Oxford University Press}
51 }]]></citation>
52 </citations>
53 </tool>