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author mingchen0919
date Fri, 14 Dec 2018 00:21:26 -0500
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1 <tool name="aurora_deseq2" id='aurora_deseq2_report' version="2.2.2">
2 <description>
3 Differential analysis of count data with the DESeq2 package
4 </description>
5 <requirements>
6 <requirement type="package" version="2.5">pandoc</requirement>
7 <requirement type="package" version="1.20.2">r-getopt</requirement>
8 <requirement type="package" version="1.10">r-rmarkdown</requirement>
9 <requirement type="package" version="1.16.1">bioconductor-deseq2</requirement>
10 <requirement type="package" version="4.5.6">r-plotly</requirement>
11 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
12 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
13 <requirement type="package" version="0.4">r-dt</requirement>
14 </requirements>
15 <command><![CDATA[
16
17 ######### each aurora tool generates a html file and have an files path directory associated with it.
18 mkdir -p $report.files_path &&
19
20 ######### three important paths:
21 ######### 1. path to tool installation directory
22 ######### 2. path to report html
23 ######### 3. path to files_path directory associated with the report output.
24 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
25 export REPORT='$report' &&
26 export REPORT_FILES_PATH='$report.files_path' &&
27
28 ############ create a hidden file to store r markdown rendering log
29 touch $report.files_path/r_rendering.log.txt &&
30
31 ############ finally run the render.R script
32 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
33
34 -o $report
35 -d $report.files_path
36 -A '$count_data'
37 -B '$column_data'
38 -C '$design_formula'
39 -D '$treatment_name'
40 -E '$treated'
41 -F '$untreated'
42 -T '$test_method'
43 -H '$fit_type'
44 -I '$alpha'
45 -J '$significant_genes'
46
47
48 ]]></command>
49 <inputs>
50 <param type="data" name="count_data" label="Count data"
51 help="The first column has feature names; The remaining columns are read counts from each sample."
52 optional="False" format="csv"/>
53 <param type="data" name="column_data" label="Column data"
54 help="The first column has sample names (column name from the count data); The remaining columns are experimental treatments."
55 optional="False" format="csv"/>
56 <param type="text" name="design_formula" label="Design formula"
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"
58 optional="False">
59 <sanitizer sanitize="true">
60 <valid initial="default">
61 <add preset="string.printable"/>
62 <add value="~"/>
63 </valid>
64 </sanitizer>
65 </param>
66 <param type="text" name="treatment_name" label="Treatment name"
67 help="one of the treatment column names from the column data." optional="False"/>
68 <param type="text" name="treated" label="Treated"
69 help="A level from the specified treatment column that will be used as the treated group in the DESeq2 analysis."
70 optional="False"/>
71 <param type="text" name="untreated" label="Untreated"
72 help="A level from the specified treatment column that will be used as the untreated group in the DESeq2 analysis."
73 optional="False"/>
74 <param type="select" name="test_method" label="Test method"
75 help="either 'Wald' or 'LRT', which will then use either Wald significance tests (defined by nbinomWaldTest),
76 or the likelihood ratio test on the difference in deviance between a full and reduced model formula (defined by nbinomLRT)">
77 <option value="Wald" selected="true">Wald</option>
78 <option value="LRT">LRT</option>
79 </param>
80 <param type="select" name="fit_type" label="Fitting of dispersions"
81 help="either &quot;parametric&quot;, &quot;local&quot;, or &quot;mean&quot; for the type of fitting of dispersions to the mean intensity"
82 optional="False">
83 <option value="parametric" selected="true">parametric</option>
84 <option value="local" selected="false">local</option>
85 <option value="mean" selected="false">mean</option>
86 </param>
87 <param type="float" name="alpha" label="Alpha"
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."
89 optional="False" value="0.1" min="0" max="1"/>
90 </inputs>
91 <outputs>
92 <data format="html" name="report" label="${tool.name} report on ${on_string}"/>
93 <data name="significant_genes" format="tabular" label="${tool.name} signficant genes on ${on_string} "
94 hidden="false"/>
95 </outputs>
96 <citations>
97 <citation type="bibtex"><![CDATA[
98 @article{allaire2016rmarkdown,
99 title={rmarkdown: Dynamic Documents for R, 2016},
100 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
101 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
102 journal={R package version 0.9},
103 volume={6},
104 year={2016}
105 }
106 ]]></citation>
107 <citation type="bibtex"><![CDATA[
108 @book{xie2015dynamic,
109 title={Dynamic Documents with R and knitr},
110 author={Xie, Yihui},
111 volume={29},
112 year={2015},
113 publisher={CRC Press}
114 }
115 ]]></citation>
116 <citation type="bibtex"><![CDATA[
117 @online{jstree,
118 author={Bozhanov, Ivan},
119 year = 2018,
120 url = {https://www.jstree.com/}
121 }
122 ]]></citation>
123 <citation type="bibtex"><![CDATA[
124 @article{love2014differential,
125 title={Differential analysis of count data--the DESeq2 package},
126 author={Love, Michael and Anders, Simon and Huber, Wolfgang},
127 journal={Genome Biol},
128 volume={15},
129 pages={550},
130 year={2014}
131 }
132 ]]></citation>
133 </citations>
134 </tool>