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comparison rmarkdown_deseq2_count_matrix.xml @ 0:c1f718dd6c7a draft

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author mingchen0919
date Sat, 30 Dec 2017 00:25:38 -0500
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1 <tool id="rmarkdown_deseq2_count_matrix" name="DESeq2 (count matrix)" 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="1.14.1">bioconductor-deseq2</requirement>
9 <requirement type="package" version="0.2">r-dt</requirement>
10 </requirements>
11 <description>deseq2 analysis given a count matrix input</description>
12 <stdio>
13 <regex source="stderr" match="XXX" level="warning"
14 description="Check the warnings_and_errors.txt file for more details."/>
15 </stdio>
16 <command><![CDATA[
17 Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrix_render.R'
18 -e $echo
19 -c $count_data
20 -C $col_data
21 -D '$design_formula'
22 -k $contrast_condition
23 -T $treatment
24 -k $control
25 -r $report
26 -d $report.files_path
27 -s $sink_message
28 -t '${__tool_directory__}/rmarkdown_deseq2_count_matrix.Rmd'
29 ]]></command>
30 <inputs>
31 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False"
32 truevalue="TRUE" falsevalue="FALSE"/>
33 <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
34 <param type="data" name="col_data" label="column data" optional="False" format="txt,csv" multiple="False"/>
35 <param type="text" name="design_formula" label="design formula"
36 help="The simplest design formula for differential expression would be ~ condition, where condition&#13;&#10; is a column in colData(dds) that specifies which of two (or more groups) the samples belong to"
37 optional="False" value="~ condition_1 + condition_2"/>
38 <param type="text" name="contrast_condition" label="condition"
39 help="A condition name specified in the design formula" optional="False" value="condition_1"/>
40 <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change"
41 optional="False"/>
42 <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
43 optional="False"/>
44 </inputs>
45 <outputs>
46 <data name="report" format="html" label="DESeq2 report" hidden="false"/>
47 <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv"
48 hidden="false"/>
49 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"
50 hidden="false"/>
51 </outputs>
52 <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>
53 <citations>
54 <citation type="bibtex"><![CDATA[ @article{love2014moderated,
55 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
56 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
57 journal={Genome biology},
58 volume={15},
59 number={12},
60 pages={550},
61 year={2014},
62 publisher={BioMed Central}
63 }]]></citation>
64 <citation type="bibtex"><![CDATA[ @article{allaire2016rmarkdown,
65 title={rmarkdown: Dynamic Documents for R, 2016},
66 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
67 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
68 journal={R package version 0.9},
69 volume={6},
70 year={2016}
71 }]]></citation>
72 </citations>
73 </tool>