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comparison DESeq_visualization.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_visualization" name="DESeq2: Visualization" 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 visualize DESeq analysis results.
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_visualization_render.R'
37
38 ## 1. input data
39 -e $echo
40 -w $deseq_workspace
41
42 #set $pca_groups = []
43 #for $group in $intgroups_pca
44 #if str($group.intgroup)
45 #set $pca_groups = $pca_groups + [str($group.intgroup)]
46 #end if
47 #end for
48 #set $pca_groups = ','.join($pca_groups)
49 -p "$pca_groups"
50
51 #set $mds_groups = []
52 #for $group in $intgroups_mds
53 #if str($group.intgroup)
54 #set $mds_groups = $mds_groups + [str($group.intgroup)]
55 #end if
56 #end for
57 #set $mds_groups = ','.join($mds_groups)
58 -m "$mds_groups"
59
60 ## 2. output report and report site directory
61 -o $deseq_visualization
62 -d $deseq_visualization.files_path
63
64
65 ## 3. Rmd templates sitting in the tool directory
66
67 ## _site.yml and index.Rmd template files
68 -D '${__tool_directory__}/DESeq_visualization.Rmd'
69
70
71
72 ]]>
73 </command>
74 <inputs>
75 <param type="data" name="deseq_workspace" format="rdata" multiple="false" label="Workspace from tool DESeq2: DESeq" />
76 <param type="data" name="sample_table" format="tabular" multiple="false" label="Sample table file" />
77 <repeat name="intgroups_pca" title="Interest groups for PCA plot" min="1">
78 <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true"
79 optional="false"
80 label="Interest group for PCA plot"
81 help=""/>
82 </repeat>
83 <repeat name="intgroups_mds" title="Interest groups for MDS plot" min="1">
84 <param type="data_column" name="intgroup" data_ref="sample_table" use_header_names="true"
85 optional="false"
86 label="Interest group for MDS plot"
87 help=""/>
88 </repeat>
89 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
90 </inputs>
91 <outputs>
92 <data name="deseq_visualization" format="html" label="DESeq Visualization" />
93 </outputs>
94 </tool>