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