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comparison DESeq.xml @ 8:3f84334c3de8 draft

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author mingchen0919
date Mon, 07 Aug 2017 18:12:02 -0400
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children 4aeffaeaaa5c
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7:a5fdd120b2c7 8:3f84334c3de8
1 <tool id="DESeq" name="DESeq2: DESeq" version="1.0.0">
2 <requirements>
3 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
4 <requirement type="package" version="1.20.0">r-getopt</requirement>
5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
6 <requirement type="package" version="1.8.4">r-plyr</requirement>
7 <requirement type="package" version="1.1.0">r-stringr</requirement>
8 <requirement type="package" version="0.4.0">r-highcharter</requirement>
9 <requirement type="package" version="0.2">r-dt</requirement>
10 <requirement type="package" version="1.4.2">r-reshape2</requirement>
11 <requirement type="package" version="4.5.6">r-plotly</requirement>
12 <requirement type="package" version="0.2.0.1">r-formattable</requirement>
13 <requirement type="package" version="0.3.5">r-htmltools</requirement>
14 </requirements>
15 <description>
16 An R Markdown tool to perform DESeq analysis.
17 </description>
18 <stdio>
19 <regex match="Execution halted"
20 source="both"
21 level="fatal"
22 description="Execution halted." />
23 <regex match="Error in"
24 source="both"
25 level="fatal"
26 description="An undefined error occured, please check your intput carefully and contact your administrator." />
27 <regex match="Fatal error"
28 source="both"
29 level="fatal"
30 description="An undefined error occured, please check your intput carefully and contact your administrator." />
31 </stdio>
32 <command>
33 <![CDATA[
34 ## Add tools to PATH
35 export PATH=/opt/R-3.2.5/bin:\$PATH &&
36
37 Rscript '${__tool_directory__}/DESeq_render.R'
38
39 ## 1. input data
40 -e $echo
41 -c $count_files
42 -s $sample_table
43 -p "$design_formula"
44
45 ## 2. output report and report site directory
46 -o $DESeq
47 -d $DESeq.files_path
48 -w $deseq_workspace
49
50 ## 3. Rmd templates sitting in the tool directory
51
52 ## _site.yml and index.Rmd template files
53 -D '${__tool_directory__}/DESeq.Rmd'
54
55
56
57 ]]>
58 </command>
59 <inputs>
60 <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count" />
61 <param type="data" name="sample_table" format="tabular" multiple="false" label="sample table file"
62 help="The sample table file contains a table. The first column is the sample name, the second column is
63 the count file name and the rest of columns are treatment columns. The file names in this table have
64 to be in the same order as the count files uploaded in the previous step. "/>
65 <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula"
66 help="The simplest design formula for differential expression would be ~ condition, where condition
67 is a column in colData(dds) that specifies which of two (or more groups) the samples belong to">
68 <sanitizer>
69 <valid initial="default">
70 <add preset="string.printable"/>
71 <add value="~"/>
72 </valid>
73 </sanitizer>
74 </param>
75 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
76 </inputs>
77 <outputs>
78 <data name="DESeq" format="html" label="DESeq Analysis" />
79 <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis" />
80 </outputs>
81 </tool>