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comparison DESeq_results.xml @ 3:ab57855151b1 draft

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author mingchen0919
date Mon, 07 Aug 2017 18:10:55 -0400
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2:cf6012738737 3:ab57855151b1
1 <tool id="DESeq_results" name="DESeq2: Results" 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 display 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_results_render.R'
38
39 ## 1. input data
40 -e $echo
41 -w $deseq_workspace
42 -c "$contrast_group"
43 -t $treatment
44 -k $condition
45
46 #set $groups = []
47 #for $c_group in $clustering_groups
48 #if str($c_group.group)
49 #set $groups = $groups + [str($c_group.group)]
50 #end if
51 #end for
52 #set $groups = ','.join($groups)
53 -m "$groups"
54
55 ## 2. output report and report site directory
56 -o $deseq_results
57 -d $deseq_results.files_path
58
59 ## 3. Rmd templates sitting in the tool directory
60
61 ## _site.yml and index.Rmd template files
62 -D '${__tool_directory__}/DESeq_results.Rmd'
63
64
65
66 ]]>
67 </command>
68 <inputs>
69 <param type="data" name="deseq_workspace" format="rdata" multiple="false" label="Workspace from tool DESeq2: DESeq" />
70 <param type="data" name="sample_table" format="tabular" multiple="false" label="Sample table file" />
71 <param type="data_column" name="contrast_group" data_ref="sample_table" use_header_names="true"
72 optional="false"
73 label="Group for result contrast"
74 help=""/>
75 <param type="text" name="treatment" label="Treatment level" />
76 <param type="text" name="condition" label="Condition level" />
77
78 <repeat name="clustering_groups" title="Gene clustering groups" min="1">
79 <param type="data_column" name="group" data_ref="sample_table" use_header_names="true"
80 optional="false"
81 label="A phenotype column from the sample table" />
82 </repeat>
83
84 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
85 </inputs>
86 <outputs>
87 <data name="deseq_results" format="html" label="DESeq Results" />
88 </outputs>
89 </tool>