|
0
|
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" description="Check the warnings_and_errors.txt file for more details."/>
|
|
|
14 </stdio>
|
|
|
15 <command><![CDATA[
|
|
|
16 Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrx_render.R'
|
|
|
17 -e $echo
|
|
|
18 -c $count_matrix
|
|
|
19 -r $report
|
|
|
20 -d $report.files_path
|
|
|
21 -s $sink_message
|
|
|
22 -t '${__tool_directory__}/rmarkdown_deseq2_count_matrx.Rmd'
|
|
|
23 ]]></command>
|
|
|
24 <inputs>
|
|
|
25 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False" truevalue="TRUE" falsevalue="FALSE"/>
|
|
|
26 <param type="data" name="count_matrix" label="count matrix" optional="False" format="txt,csv" multiple="False"/>
|
|
|
27 </inputs>
|
|
|
28 <outputs>
|
|
|
29 <data name="report" format="html" label="DESeq2 report" hidden="false"/>
|
|
|
30 <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv" hidden="false"/>
|
|
|
31 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt" hidden="false"/>
|
|
|
32 </outputs>
|
|
|
33 <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>
|
|
|
34 <citations>
|
|
|
35 <citation type="bibtex"><![CDATA[ @article{love2014moderated,
|
|
|
36 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
|
|
|
37 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
|
|
|
38 journal={Genome biology},
|
|
|
39 volume={15},
|
|
|
40 number={12},
|
|
|
41 pages={550},
|
|
|
42 year={2014},
|
|
|
43 publisher={BioMed Central}
|
|
|
44 }]]></citation>
|
|
|
45 <citation type="bibtex"><![CDATA[ @article{allaire2016rmarkdown,
|
|
|
46 title={rmarkdown: Dynamic Documents for R, 2016},
|
|
|
47 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
|
|
|
48 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
|
|
|
49 journal={R package version 0.9},
|
|
|
50 volume={6},
|
|
|
51 year={2016}
|
|
|
52 }]]></citation>
|
|
|
53 </citations>
|
|
|
54 </tool>
|
