Mercurial > repos > mingchen0919 > rmarkdown_deseq2_test

annotate DESeq_visualization.xml @ 0:61c184384d02 draft default tip

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author mingchen0919
date Tue, 07 Nov 2017 10:02:57 -0500
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1 <tool id="DESeq_visualization" name="DESeq2: Visualization" 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="1.14.1">bioconductor-deseq2</requirement>
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5 <requirement type="package" version="1.20.0">r-getopt</requirement>
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6 <requirement type="package" version="1.2">r-rmarkdown</requirement>
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7 <requirement type="package" version="1.8.4">r-plyr</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 visualize DESeq analysis results.
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19 </description>
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20 <stdio>
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21 <regex match="Execution halted"
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22 source="both"
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23 level="fatal"
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24 description="Execution halted." />
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25 <regex match="Error in"
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26 source="both"
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27 level="fatal"
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28 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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29 <regex match="Fatal error"
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30 source="both"
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31 level="fatal"
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32 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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33 </stdio>
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34 <command>
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35 <![CDATA[
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36
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37 Rscript '${__tool_directory__}/DESeq_visualization_render.R'
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38
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39 ## 1. input data
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40 -e $echo
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41 -w $deseq_workspace
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42
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43 #set $pca_groups = []
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44 #for $group in $intgroups_pca
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45 #if str($group.intgroup)
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46 #set $pca_groups = $pca_groups + [str($group.intgroup)]
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47 #end if
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48 #end for
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49 #set $pca_groups = ','.join($pca_groups)
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50 -p "$pca_groups"
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51
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52 #set $mds_groups = []
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53 #for $group in $intgroups_mds
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54 #if str($group.intgroup)
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55 #set $mds_groups = $mds_groups + [str($group.intgroup)]
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56 #end if
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57 #end for
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58 #set $mds_groups = ','.join($mds_groups)
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59 -m "$mds_groups"
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60
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61 ## 2. output report and report site directory
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62 -o $deseq_visualization
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63 -d $deseq_visualization.files_path
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64
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65
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66 ## 3. Rmd templates sitting in the tool directory
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67
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68 ## _site.yml and index.Rmd template files
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69 -D '${__tool_directory__}/DESeq_visualization.Rmd'
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70
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71
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72
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73 ]]>
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74 </command>
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75 <inputs>
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76 <param type="data" name="deseq_workspace" format="rdata" multiple="false" label="Workspace from tool DESeq2: DESeq" />
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77 <param type="data" name="sample_table" format="tabular" multiple="false" label="Sample table file" />
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78 <repeat name="intgroups_pca" title="Interest groups for PCA plot" min="1">
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79 <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true"
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80 optional="false"
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81 label="Interest group for PCA plot"
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82 help=""/>
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83 </repeat>
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84 <repeat name="intgroups_mds" title="Interest groups for MDS plot" min="1">
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85 <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true"
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86 optional="false"
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87 label="Interest group for MDS plot"
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88 help=""/>
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89 </repeat>
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90 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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91 </inputs>
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92 <outputs>
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93 <data name="deseq_visualization" format="html" label="DESeq Visualization" />
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94 </outputs>
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95 <citations>
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96 <citation>
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97 @article{love2014moderated,
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98 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
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99 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
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100 journal={Genome biology},
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101 volume={15},
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102 number={12},
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103 pages={550},
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104 year={2014},
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105 publisher={BioMed Central}
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106 }
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107 </citation>
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108 <citation type="bibtex">
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109 @article{allaire2016rmarkdown,
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110 title={rmarkdown: Dynamic Documents for R, 2016},
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111 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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112 journal={R package version 0.9},
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113 volume={6},
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114 year={2016}
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115 }
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116 </citation>
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117 <citation type="bibtex">
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118 @book{xie2015dynamic,
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119 title={Dynamic Documents with R and knitr},
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120 author={Xie, Yihui},
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121 volume={29},
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122 year={2015},
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123 publisher={CRC Press}
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124 }
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125 </citation>
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126 <citation>
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127 @misc{pheatmap2015,
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128 title = {pheatmap: Pretty Heatmaps},
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129 author = {Raivo Kolde},
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130 year = {2015},
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131 note = {R package version 1.0.8},
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132 url = {https://CRAN.R-project.org/package=pheatmap},
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133 }
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134 </citation>
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135 <citation>
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136 @misc{dt2016,
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137 title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
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138 author = {Yihui Xie},
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139 year = {2016},
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140 note = {R package version 0.2},
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141 url = {https://CRAN.R-project.org/package=DT},
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142 }
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143 </citation>
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144 </citations>
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145 </tool>