Mercurial > repos > mingchen0919 > aurora_deseq2

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author mingchen0919
date Sun, 30 Dec 2018 14:04:26 -0500
parents 55d2db17c67c
children
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1 <tool name="aurora_deseq2" id='aurora_deseq2_report' version="2.2.2">
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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>
1
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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="1.16.1">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 <requirement type="package" version="0.4">r-dt</requirement>
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14 </requirements>
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15 <command><![CDATA[
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16
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17 ######### each aurora tool generates a html file and have an files path directory associated with it.
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18 mkdir -p $report.files_path &&
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19
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20 ######### three important paths:
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21 ######### 1. path to tool installation directory
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22 ######### 2. path to report html
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23 ######### 3. path to files_path directory associated with the report output.
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24 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
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25 export REPORT='$report' &&
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26 export REPORT_FILES_PATH='$report.files_path' &&
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27
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28 ############ create a hidden file to store r markdown rendering log
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29 touch $report.files_path/r_rendering.log.txt &&
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30
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31 ############ finally run the render.R script
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32 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
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33
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34 -o $report
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35 -d $report.files_path
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36 -A '$count_data'
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37 -B '$column_data'
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38 -C '$design_formula'
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39 -D '$treatment_name'
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40 -E '$treated'
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41 -F '$untreated'
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42 -T '$test_method'
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43 -H '$fit_type'
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44 -I '$alpha'
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45 -J '$significant_genes'
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46
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47
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48 ]]></command>
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49 <inputs>
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50 <param type="data" name="count_data" label="Count data"
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51 help="The first column has feature names; The remaining columns are read counts from each sample."
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52 optional="False" format="csv"/>
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53 <param type="data" name="column_data" label="Column data"
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54 help="The first column has sample names (column name from the count data); The remaining columns are experimental treatments."
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55 optional="False" format="csv"/>
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56 <param type="text" name="design_formula" label="Design formula"
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57 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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58 optional="False">
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59 <sanitizer sanitize="true">
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60 <valid initial="default">
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61 <add preset="string.printable"/>
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62 <add value="~"/>
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63 </valid>
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64 </sanitizer>
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65 </param>
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66 <param type="text" name="treatment_name" label="Treatment name"
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67 help="one of the treatment column names from the column data." optional="False"/>
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68 <param type="text" name="treated" label="Treated"
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69 help="A level from the specified treatment column that will be used as the treated group in the DESeq2 analysis."
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70 optional="False"/>
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71 <param type="text" name="untreated" label="Untreated"
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72 help="A level from the specified treatment column that will be used as the untreated group in the DESeq2 analysis."
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73 optional="False"/>
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74 <param type="select" name="test_method" label="Test method"
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75 help="either 'Wald' or 'LRT', which will then use either Wald significance tests (defined by nbinomWaldTest),
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76 or the likelihood ratio test on the difference in deviance between a full and reduced model formula (defined by nbinomLRT)">
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77 <option value="Wald" selected="true">Wald</option>
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78 <option value="LRT">LRT</option>
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79 </param>
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80 <param type="select" name="fit_type" label="Fitting of dispersions"
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81 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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82 optional="False">
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83 <option value="parametric" selected="true">parametric</option>
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84 <option value="local" selected="false">local</option>
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85 <option value="mean" selected="false">mean</option>
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86 </param>
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87 <param type="float" name="alpha" label="Alpha"
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88 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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89 optional="False" value="0.1" min="0" max="1"/>
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90 </inputs>
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91 <outputs>
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92 <data format="html" name="report" label="${tool.name} report on ${on_string}"/>
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93 <data name="significant_genes" format="tabular" label="${tool.name} signficant genes on ${on_string} "
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94 hidden="false"/>
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95 </outputs>
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96 <citations>
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97 <citation type="bibtex"><![CDATA[
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98 @article{allaire2016rmarkdown,
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99 title={rmarkdown: Dynamic Documents for R, 2016},
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100 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
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101 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
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102 journal={R package version 0.9},
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103 volume={6},
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104 year={2016}
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105 }
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106 ]]></citation>
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107 <citation type="bibtex"><![CDATA[
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108 @book{xie2015dynamic,
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109 title={Dynamic Documents with R and knitr},
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110 author={Xie, Yihui},
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111 volume={29},
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112 year={2015},
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113 publisher={CRC Press}
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114 }
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115 ]]></citation>
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116 <citation type="bibtex"><![CDATA[
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117 @online{jstree,
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118 author={Bozhanov, Ivan},
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119 year = 2018,
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120 url = {https://www.jstree.com/}
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121 }
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122 ]]></citation>
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123 <citation type="bibtex"><![CDATA[
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124 @article{love2014differential,
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125 title={Differential analysis of count data--the DESeq2 package},
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126 author={Love, Michael and Anders, Simon and Huber, Wolfgang},
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127 journal={Genome Biol},
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128 volume={15},
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129 pages={550},
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130 year={2014}
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131 }
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132 ]]></citation>
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133 </citations>
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134 </tool>