Mercurial > repos > mingchen0919 > rmarkdown_deseq2

annotate DESeq_results.xml @ 7:466053167103 draft

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update deseq2
author mingchen0919
date Tue, 07 Nov 2017 13:51:10 -0500
parents 2f8ddef8d545
children 5f7665898fd9
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1 <tool id="DESeq_results" name="DESeq2: Results" version="2.0.0">
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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="1.2">r-rmarkdown</requirement>
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6 <requirement type="package" version="1.8.4">r-plyr</requirement>
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7 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
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8 <requirement type="package" version="1.1.0">r-stringr</requirement>
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9 <requirement type="package" version="0.4.0">r-highcharter</requirement>
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10 <requirement type="package" version="0.2">r-dt</requirement>
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11 <requirement type="package" version="1.4.2">r-reshape2</requirement>
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12 <requirement type="package" version="4.5.6">r-plotly</requirement>
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13 <requirement type="package" version="0.2.0.1">r-formattable</requirement>
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14 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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15 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
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16 </requirements>
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17 <description>
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18 An R Markdown tool to display DESeq analysis.
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19 </description>
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20 <stdio>
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21 <!--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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22 <regex match="XXX"
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23 source="stderr"
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24 level="warning"
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25 description="Check the warnings_and_errors.txt file for more details."/>
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26 </stdio>
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27 <command>
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28 <![CDATA[
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30 Rscript '${__tool_directory__}/DESeq_results_render.R'
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32 ## 1. input data
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33 -e $echo
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34 -W $deseq_workspace
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35 -C '$contrast_factor'
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36 -T '$treatment'
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37 -K '$condition'
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38
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39 -M '$clustering_factors'
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41 ## 2. output report and report site directory
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42 -r $report
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43 -d $report.files_path
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44 -s $sink_message
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45 -R $deseq_results
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47 ## 3. Rmd templates sitting in the tool directory
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48 -t '${__tool_directory__}/DESeq_results.Rmd'
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52 ]]>
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53 </command>
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54 <inputs>
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55 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
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56 label="Display analysis code in report?"/>
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57 <param type="data" name="deseq_workspace" format="rdata" multiple="false" optional="false"
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58 label="Workspace from tool DESeq2: DESeq"/>
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59 <param type="text" name="contrast_factor" label="Factor" optional="false"
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60 help="the name of a factor in the design formula"/>
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61 <param type="text" name="treatment" label="Treatment level" optional="false"
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62 help=" the name of the numerator level for the fold change"/>
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63 <param type="text" name="condition" label="Condition level" optional="false"
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64 help=" the name of the denominator level for the fold change"/>
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65 <param type="text" name="clustering_factors" title="Gene clustering factors" optional="false"
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66 label="factors of interest for clustering samples and PCA plot"
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67 help="A single factor or multiple factors from the design formula. Multiple factors are separated by comma (,)."/>
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68 </inputs>
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69 <outputs>
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70 <data format="html" name="report" label="DESeq results report on ${on_string}" />
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71 <data format="txt" name="sink_message" label="Warnings and Errors on ${on_string}" from_work_dir="warnings_and_errors.txt"/>
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72 <data format="csv" name="deseq_results" label="DESeq results on ${on_string}" from_work_dir="deseq_results.csv" />
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73 </outputs>
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74 <citations>
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75 <citation>
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76 @article{love2014moderated,
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77 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
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78 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
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79 journal={Genome biology},
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80 volume={15},
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81 number={12},
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82 pages={550},
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83 year={2014},
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84 publisher={BioMed Central}
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85 }
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86 </citation>
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87 <citation type="bibtex">
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88 @article{allaire2016rmarkdown,
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89 title={rmarkdown: Dynamic Documents for R, 2016},
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90 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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91 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
3
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92 journal={R package version 0.9},
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93 volume={6},
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94 year={2016}
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95 }
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96 </citation>
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97 <citation type="bibtex">
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98 @book{xie2015dynamic,
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99 title={Dynamic Documents with R and knitr},
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100 author={Xie, Yihui},
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101 volume={29},
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102 year={2015},
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103 publisher={CRC Press}
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104 }
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105 </citation>
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106 <citation>
6
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107 @article{love2014moderated,
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108 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
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109 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
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110 journal={Genome biology},
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111 volume={15},
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112 number={12},
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113 pages={550},
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114 year={2014},
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115 publisher={BioMed Central}
3
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116 }
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117 </citation>
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118 </citations>
0
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119 </tool>