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"
+ − 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 $count_data
1
+ − 20 -n '$count_matrix_column_names'
0
+ − 21 -C $col_data
+ − 22 -D '$design_formula'
+ − 23 -k $contrast_condition
+ − 24 -T $treatment
1
+ − 25 -K $control
0
+ − 26 -r $report
+ − 27 -d $report.files_path
+ − 28 -s $sink_message
+ − 29 -t '${__tool_directory__}/rmarkdown_deseq2_count_matrix.Rmd'
+ − 30 ]]></command>
+ − 31 <inputs>
+ − 32 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False"
+ − 33 truevalue="TRUE" falsevalue="FALSE"/>
+ − 34 <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
1
+ − 35 <param type="text" name="count_matrix_column_names" label="column names"
+ − 36 help="This field is used to update the column names of count data matrix. Column names are separated by comma (,). For example, 'column_1, column_2, column_3, column_4'"
+ − 37 optional="True" area="True" size="5x25"></param>
2
+ − 38 <param type="data" name="col_data" label="column data (from file)" optional="False" format="csv" multiple="False"/>
0
+ − 39 <param type="text" name="design_formula" label="design formula"
+ − 40 help="The simplest design formula for differential expression would be ~ condition, where condition is a column in colData(dds) that specifies which of two (or more groups) the samples belong to"
1
+ − 41 optional="False" value="~ condition_1 + condition_2">
+ − 42 <sanitizer>
+ − 43 <valid>
+ − 44 <add value="~"/>
+ − 45 </valid>
+ − 46 </sanitizer>
+ − 47 </param>
0
+ − 48 <param type="text" name="contrast_condition" label="condition"
+ − 49 help="A condition name specified in the design formula" optional="False" value="condition_1"/>
+ − 50 <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change"
1
+ − 51 optional="False" value="treated"/>
0
+ − 52 <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
1
+ − 53 optional="False" value="untreated"/>
0
+ − 54 </inputs>
+ − 55 <outputs>
+ − 56 <data name="report" format="html" label="DESeq2 report" hidden="false"/>
+ − 57 <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv"
+ − 58 hidden="false"/>
1
+ − 59 <data name="deseq2" format="rdata" label="DESeq2 R objects" from_work_dir="deseq2.RData"
+ − 60 hidden="false"/>
0
+ − 61 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"
+ − 62 hidden="false"/>
+ − 63 </outputs>
+ − 64 <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>
+ − 65 <citations>
+ − 66 <citation type="bibtex"><![CDATA[ @article{love2014moderated,
+ − 67 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
+ − 68 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
+ − 69 journal={Genome biology},
+ − 70 volume={15},
+ − 71 number={12},
+ − 72 pages={550},
+ − 73 year={2014},
+ − 74 publisher={BioMed Central}
+ − 75 }]]></citation>
+ − 76 <citation type="bibtex"><![CDATA[ @article{allaire2016rmarkdown,
+ − 77 title={rmarkdown: Dynamic Documents for R, 2016},
+ − 78 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+ − 79 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+ − 80 journal={R package version 0.9},
+ − 81 volume={6},
+ − 82 year={2016}
+ − 83 }]]></citation>
+ − 84 </citations>
+ − 85 </tool>