Mercurial > repos > mingchen0919 > aurora_deseq2_site

annotate rmarkdown_report.xml @ 1:32210899a3dd draft

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author mingchen0919
date Sun, 30 Dec 2018 12:45:56 -0500
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children ab8d558ea6e6
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1 <tool name="aurora_deseq2_site" id='aurora_deseq2_site_report' version="2.2.1">
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2 <description>
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3 Differential analysis of count data with the DESeq2 package
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
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7 <requirement type="package" version="1.20.0">r-getopt</requirement>
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8 <requirement type="package" version="1.6">r-rmarkdown</requirement>
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9 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
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10 <requirement type="package" version="4.5.6">r-plotly</requirement>
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11 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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12 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
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13 </requirements>
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14 <command><![CDATA[
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15
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16 ######### each aurora tool generates a html file and have an files path directory associated with it.
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17 mkdir -p $report.files_path &&
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18
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19 ######### three important paths:
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20 ######### 1. path to tool installation directory
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21 ######### 2. path to report html
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22 ######### 3. path to files_path directory associated with the report output.
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23 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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24 export REPORT='$report' &&
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25 export REPORT_FILES_PATH='$report.files_path' &&
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26
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27 ############ create a hidden file to store r markdown rendering log
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28 touch $report.files_path/.r_rendering.log.txt &&
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29
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30 ############ finally run the render.R script
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31 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
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32
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33 -o $report
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34 -d $report.files_path
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35 -A '$count_data'
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36 -B '$column_data'
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37 -C '$design_formula'
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38 -D '$treatment_name'
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39 -E '$treated'
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40 -F '$untreated'
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41 -G '$test_type'
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42 -H '$fit_type'
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43 -I '$alpha'
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44 -J '$significant_genes'
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45
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46
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47 ]]></command>
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48 <inputs>
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49 <param type="data" name="count_data" label="Count data"
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50 help="The first column is sample names; The remaining columns are read counts from each sample."
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51 optional="False" format="csv"/>
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52 <param type="data" name="column_data" label="Column data"
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53 help="The first column are sample names (column name from the count data); The remaining columns are experimental treatments."
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54 optional="False" format="csv"/>
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55 <param type="text" name="design_formula" label="Design formula"
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56 help="The design formula expresses the variables which will be used in modeling. The formula should be a tilde (~) followed by the variables with plus signs between them, e.g., ~ condition1 + condition2"
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57 optional="False">
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58 <sanitizer sanitize="true">
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59 <valid initial="default">
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60 <add preset="string.printable"/>
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61 <add value="~"/>
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62 </valid>
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63 </sanitizer>
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64 </param>
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65 <param type="text" name="treatment_name" label="Treatment name"
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66 help="one of the treatment column names from the column data." optional="False"/>
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67 <param type="text" name="treated" label="Treated"
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68 help="A level from the specified treatment column that will be used as the treated group in the DESeq2 analysis."
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69 optional="False"/>
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70 <param type="text" name="untreated" label="Untreated"
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71 help="A level from the specified treatment column that will be used as the untreated group in the DESeq2 analysis."
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72 optional="False"/>
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73 <param type="select" name="test_type" label="Test type" optional="False">
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74 <option value="Wald" selected="true">Wald</option>
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75 <option value="LRT" selected="false">Likelihood Ratio Test (LRT)</option>
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76 </param>
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77 <param type="select" name="fit_type" label="Fitting of dispersions"
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78 help="either &quot;parametric&quot;, &quot;local&quot;, or &quot;mean&quot; for the type of fitting of dispersions to the mean intensity"
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79 optional="False">
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80 <option value="parametric" selected="true">parametric</option>
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81 <option value="local" selected="false">local</option>
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82 <option value="mean" selected="false">mean</option>
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83 </param>
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84 <param type="float" name="alpha" label="Alpha"
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85 help="the significance cutoff used for optimizing the independent filtering (by default 0.1). If the adjusted p-value cutoff (FDR) will be a value other than 0.1, alpha should be set to that value."
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86 optional="False" value="0.1" min="0" max="1"/>
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87 </inputs>
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88 <outputs>
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89 <data format="html" name="report" label="${tool.name} on ${on_string}"/>
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90 <data name="significant_genes" format="tabular" label="${tool.name} signficant genes on ${on_string} "
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91 hidden="false"/>
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92 </outputs>
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93 <citations>
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94 <citation type="bibtex"><![CDATA[
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95 @article{allaire2016rmarkdown,
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96 title={rmarkdown: Dynamic Documents for R, 2016},
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97 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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98 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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99 journal={R package version 0.9},
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100 volume={6},
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101 year={2016}
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102 }
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103 ]]></citation>
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104 <citation type="bibtex"><![CDATA[
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105 @book{xie2015dynamic,
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106 title={Dynamic Documents with R and knitr},
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107 author={Xie, Yihui},
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108 volume={29},
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109 year={2015},
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110 publisher={CRC Press}
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111 }
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112 ]]></citation>
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113 <citation type="bibtex"><![CDATA[
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114 @online{jstree,
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115 author={Bozhanov, Ivan},
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116 year = 2018,
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117 url = {https://www.jstree.com/}
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118 }
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119 ]]></citation>
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120 <citation type="bibtex"><![CDATA[
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121 @article{love2014differential,
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122 title={Differential analysis of count data--the DESeq2 package},
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123 author={Love, Michael and Anders, Simon and Huber, Wolfgang},
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124 journal={Genome Biol},
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125 volume={15},
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126 pages={550},
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127 year={2014}
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128 }
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129 ]]></citation>
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130 </citations>
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131 </tool>