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comparison DESeq.xml @ 0:7231d7e8d3ed draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_deseq2 commit 9285c2b8ad41a486dde2a87600a6b8267841c8b5-dirty
author mingchen0919
date Tue, 08 Aug 2017 10:43:18 -0400
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children 15a5fb1a2ac8
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-1:000000000000 0:7231d7e8d3ed
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 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
15 </requirements>
16 <description>
17 An R Markdown tool to perform DESeq analysis.
18 </description>
19 <stdio>
20 <regex match="Execution halted"
21 source="both"
22 level="fatal"
23 description="Execution halted." />
24 <regex match="Error in"
25 source="both"
26 level="fatal"
27 description="An undefined error occured, please check your intput carefully and contact your administrator." />
28 <regex match="Fatal error"
29 source="both"
30 level="fatal"
31 description="An undefined error occured, please check your intput carefully and contact your administrator." />
32 </stdio>
33 <command>
34 <![CDATA[
35
36 Rscript '${__tool_directory__}/DESeq_render.R'
37
38 ## 1. input data
39 -e $echo
40 -c $count_files
41 -s $sample_table
42 -p "$design_formula"
43
44 ## 2. output report and report site directory
45 -o $DESeq
46 -d $DESeq.files_path
47 -w $deseq_workspace
48
49 ## 3. Rmd templates sitting in the tool directory
50
51 ## _site.yml and index.Rmd template files
52 -D '${__tool_directory__}/DESeq.Rmd'
53
54
55
56 ]]>
57 </command>
58 <inputs>
59 <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count" />
60 <param type="data" name="sample_table" format="tabular" multiple="false" label="sample table file"
61 help="The sample table file contains a table. The first column is the sample name, the second column is
62 the count file name and the rest of columns are treatment columns. The file names in this table have
63 to be in the same order as the count files uploaded in the previous step. "/>
64 <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula"
65 help="The simplest design formula for differential expression would be ~ condition, where condition
66 is a column in colData(dds) that specifies which of two (or more groups) the samples belong to">
67 <sanitizer>
68 <valid initial="default">
69 <add preset="string.printable"/>
70 <add value="~"/>
71 </valid>
72 </sanitizer>
73 </param>
74 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
75 </inputs>
76 <outputs>
77 <data name="DESeq" format="html" label="DESeq Analysis" />
78 <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis" />
79 </outputs>
80 </tool>