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1 <tool id="deseq_results" name="DESeq2: Results" version="2.0.1">
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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="1.6">r-rmarkdown</requirement>
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6 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
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7 <requirement type="package" version="0.2">r-dt</requirement>
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8 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
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9 </requirements>
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10 <description>
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11 display DESeq2 analysis results.
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12 </description>
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13 <stdio>
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14 <!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
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15 <regex match="XXX"
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16 source="stderr"
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17 level="warning"
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18 description="Check the warnings_and_errors.txt file for more details."/>
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19 </stdio>
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20 <command>
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21 <![CDATA[
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22
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23 Rscript '${__tool_directory__}/DESeq_results_render.R'
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24
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25 -e $echo
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26 -o $report
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27 -d $report.files_path
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28 -s $sink_message
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29 -t '${__tool_directory__}'
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30
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31 ## 1. input data
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32
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33 -W $deseq_workspace
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34 -C '$contrast_factor'
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35 -T '$treatment'
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36 -K '$condition'
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37
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38 -M '$clustering_factors'
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39
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40 ## 2. output report and report site directory
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41 -R $deseq_results
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42
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43
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44 ]]>
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45 </command>
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46 <inputs>
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47 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
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48 label="Display analysis code in report?"/>
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49 <param type="data" name="deseq_workspace" format="rdata" multiple="false" optional="false"
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50 label="Workspace from tool DESeq2: DESeq"/>
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51 <param type="text" name="contrast_factor" label="Factor" optional="false"
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52 help="the name of a factor in the design formula"/>
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53 <param type="text" name="treatment" label="Treatment level" optional="false"
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54 help=" the name of the numerator level for the fold change"/>
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55 <param type="text" name="condition" label="Condition level" optional="false"
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56 help=" the name of the denominator level for the fold change"/>
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57 <param type="text" name="clustering_factors" title="Gene clustering factors" optional="false"
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58 label="factors of interest for clustering samples and PCA plot"
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59 help="A single factor or multiple factors from the design formula. Multiple factors are separated by comma (,)."/>
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60 </inputs>
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61 <outputs>
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62 <data format="html" name="report" label="DESeq results report on ${on_string}" />
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63 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
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64 <data format="csv" name="deseq_results" label="DESeq results on ${on_string}" from_work_dir="deseq_results.csv" />
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65 </outputs>
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66 <citations>
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67 <citation type="bibtex">
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68 @article{love2014moderated,
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69 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
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70 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
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71 journal={Genome biology},
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72 volume={15},
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73 number={12},
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74 pages={550},
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75 year={2014},
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76 publisher={BioMed Central}
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77 }
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78 </citation>
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79 <citation type="bibtex">
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80 @article{allaire2016rmarkdown,
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81 title={rmarkdown: Dynamic Documents for R, 2016},
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82 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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83 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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84 journal={R package version 0.9},
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85 volume={6},
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86 year={2016}
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87 }
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88 </citation>
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89 <citation type="bibtex">
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90 @book{xie2015dynamic,
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91 title={Dynamic Documents with R and knitr},
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92 author={Xie, Yihui},
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93 volume={29},
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94 year={2015},
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95 publisher={CRC Press}
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96 }
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97 </citation>
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98 </citations>
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99 </tool> |
