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1 <tool id="rmarkdown_deseq2_count_matrix" name="DESeq2 (count matrix)" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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4 <requirement type="package" version="1.20.0">r-getopt</requirement>
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5 <requirement type="package" version="1.3">r-rmarkdown</requirement>
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6 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
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8 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
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9 <requirement type="package" version="0.2">r-dt</requirement>
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10 </requirements>
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11 <description>deseq2 analysis given a count matrix input</description>
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12 <stdio>
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13 <regex source="stderr" match="XXX" level="warning"
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14 description="Check the warnings_and_errors.txt file for more details."/>
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15 </stdio>
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16 <command><![CDATA[
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17 Rscript '${__tool_directory__}/rmarkdown_deseq2_count_matrix_render.R'
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18 -e $echo
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19 -c $count_data
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20 -C $col_data
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21 -D '$design_formula'
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22 -k $contrast_condition
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23 -T $treatment
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24 -k $control
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25 -r $report
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26 -d $report.files_path
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27 -s $sink_message
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28 -t '${__tool_directory__}/rmarkdown_deseq2_count_matrix.Rmd'
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29 ]]></command>
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30 <inputs>
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31 <param type="boolean" name="echo" label="Display analysis code in report?" optional="False" checked="False"
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32 truevalue="TRUE" falsevalue="FALSE"/>
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33 <param type="data" name="count_data" label="count data" optional="False" format="txt,csv" multiple="False"/>
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34 <param type="data" name="col_data" label="column data" optional="False" format="txt,csv" multiple="False"/>
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35 <param type="text" name="design_formula" label="design formula"
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36 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"
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37 optional="False" value="~ condition_1 + condition_2"/>
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38 <param type="text" name="contrast_condition" label="condition"
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39 help="A condition name specified in the design formula" optional="False" value="condition_1"/>
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40 <param type="text" name="treatment" label="treatment" help="the name of the numerator level for the fold change"
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41 optional="False"/>
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42 <param type="text" name="control" label="control" help="the name of the denominator level for the fold change"
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43 optional="False"/>
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44 </inputs>
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45 <outputs>
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46 <data name="report" format="html" label="DESeq2 report" hidden="false"/>
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47 <data name="differential_genes" format="csv" label="differential genes" from_work_dir="differential_genes.csv"
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48 hidden="false"/>
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49 <data name="sink_message" format="txt" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"
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50 hidden="false"/>
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51 </outputs>
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52 <help><![CDATA[See http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html]]></help>
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53 <citations>
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54 <citation type="bibtex"><![CDATA[ @article{love2014moderated,
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55 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
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56 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
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57 journal={Genome biology},
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58 volume={15},
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59 number={12},
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60 pages={550},
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61 year={2014},
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62 publisher={BioMed Central}
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63 }]]></citation>
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64 <citation type="bibtex"><![CDATA[ @article{allaire2016rmarkdown,
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65 title={rmarkdown: Dynamic Documents for R, 2016},
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66 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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67 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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68 journal={R package version 0.9},
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69 volume={6},
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70 year={2016}
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71 }]]></citation>
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72 </citations>
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73 </tool>
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