Mercurial > repos > mingchen0919 > rmarkdown_deseq2

annotate DESeq.xml @ 3:15a5fb1a2ac8 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
author mingchen0919
date Tue, 08 Aug 2017 11:45:42 -0400
parents 7231d7e8d3ed
children 7f0281d26b81
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7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
mingchen0919
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1 <tool id="DESeq" name="DESeq2: DESeq" version="1.0.0">
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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2 <requirements>
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3 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
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4 <requirement type="package" version="1.20.0">r-getopt</requirement>
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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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="1.1.0">r-stringr</requirement>
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8 <requirement type="package" version="0.4.0">r-highcharter</requirement>
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9 <requirement type="package" version="0.2">r-dt</requirement>
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10 <requirement type="package" version="1.4.2">r-reshape2</requirement>
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11 <requirement type="package" version="4.5.6">r-plotly</requirement>
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12 <requirement type="package" version="0.2.0.1">r-formattable</requirement>
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13 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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14 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
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15 </requirements>
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16 <description>
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17 An R Markdown tool to perform DESeq analysis.
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18 </description>
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19 <stdio>
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20 <regex match="Execution halted"
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21 source="both"
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22 level="fatal"
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23 description="Execution halted." />
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24 <regex match="Error in"
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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25 source="both"
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26 level="fatal"
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27 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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28 <regex match="Fatal error"
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29 source="both"
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30 level="fatal"
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31 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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32 </stdio>
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33 <command>
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34 <![CDATA[
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35
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36 Rscript '${__tool_directory__}/DESeq_render.R'
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37
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38 ## 1. input data
7231d7e8d3ed planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
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39 -e $echo
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40 -c $count_files
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41 -s $sample_table
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42 -p "$design_formula"
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43
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44 ## 2. output report and report site directory
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45 -o $DESeq
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46 -d $DESeq.files_path
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47 -w $deseq_workspace
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48
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49 ## 3. Rmd templates sitting in the tool directory
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50
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51 ## _site.yml and index.Rmd template files
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52 -D '${__tool_directory__}/DESeq.Rmd'
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53
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54
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55
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56 ]]>
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57 </command>
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58 <inputs>
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59 <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count" />
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60 <param type="data" name="sample_table" format="tabular" multiple="false" label="sample table file"
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61 help="The sample table file contains a table. The first column is the sample name, the second column is
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62 the count file name and the rest of columns are treatment columns. The file names in this table have
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63 to be in the same order as the count files uploaded in the previous step. "/>
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64 <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula"
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65 help="The simplest design formula for differential expression would be ~ condition, where condition
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66 is a column in colData(dds) that specifies which of two (or more groups) the samples belong to">
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67 <sanitizer>
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68 <valid initial="default">
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69 <add preset="string.printable"/>
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70 <add value="~"/>
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71 </valid>
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72 </sanitizer>
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73 </param>
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74 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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75 </inputs>
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76 <outputs>
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77 <data name="DESeq" format="html" label="DESeq Analysis" />
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78 <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis" />
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79 </outputs>
3
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80 <citations>
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81 <citation>
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82 @article{love2014moderated,
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83 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
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84 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
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85 journal={Genome biology},
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86 volume={15},
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87 number={12},
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88 pages={550},
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89 year={2014},
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90 publisher={BioMed Central}
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91 }
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92 </citation>
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93 <citation type="bibtex">
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94 @article{allaire2016rmarkdown,
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95 title={rmarkdown: Dynamic Documents for R, 2016},
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96 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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97 journal={R package version 0.9},
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98 volume={6},
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99 year={2016}
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100 }
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101 </citation>
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102 <citation type="bibtex">
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103 @book{xie2015dynamic,
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104 title={Dynamic Documents with R and knitr},
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105 author={Xie, Yihui},
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106 volume={29},
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107 year={2015},
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108 publisher={CRC Press}
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109 }
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110 </citation>
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111 <citation>
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112 @misc{pheatmap2015,
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113 title = {pheatmap: Pretty Heatmaps},
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114 author = {Raivo Kolde},
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115 year = {2015},
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116 note = {R package version 1.0.8},
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117 url = {https://CRAN.R-project.org/package=pheatmap},
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118 }
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119 </citation>
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120 <citation>
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121 @misc{dt2016,
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122 title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
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123 author = {Yihui Xie},
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124 year = {2016},
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125 note = {R package version 0.2},
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126 url = {https://CRAN.R-project.org/package=DT},
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127 }
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128 </citation>
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129 </citations>
0
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130 </tool>