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comparison wgcna_eigengene_visualization.xml @ 0:4275479ada3a draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
author mingchen0919
date Tue, 08 Aug 2017 12:35:50 -0400
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1 <tool id="wgcna_eigengene_visualization" name="WGCNA: eigengene visualization" version="1.0.0">
2 <requirements>
3 <requirement type="package" version="1.20.0">r-getopt</requirement>
4 <requirement type="package" version="1.2">r-rmarkdown</requirement>
5 <requirement type="package" version="1.8.4">r-plyr</requirement>
6 <requirement type="package" version="0.4.0">r-highcharter</requirement>
7 <requirement type="package" version="0.2">r-dt</requirement>
8 <requirement type="package" version="0.3.5">r-htmltools</requirement>
9 <requirement type="package" version="1.51">r-wgcna</requirement>
10 </requirements>
11 <description>
12 Eigengene visualization.
13 </description>
14 <stdio>
15 <regex match="Execution halted"
16 source="both"
17 level="fatal"
18 description="Execution halted." />
19 <regex match="Error in"
20 source="both"
21 level="fatal"
22 description="An undefined error occured, please check your intput carefully and contact your administrator." />
23 <regex match="Fatal error"
24 source="both"
25 level="fatal"
26 description="An undefined error occured, please check your intput carefully and contact your administrator." />
27 </stdio>
28 <command>
29 <![CDATA[
30 ## Add tools to PATH
31 export PATH=/opt/R-3.2.5/bin:\$PATH &&
32
33 Rscript '${__tool_directory__}/wgcna_eigengene_visualization_render.R'
34
35 ## 1. input data
36 -e $echo
37 -w $construct_network_workspace
38 -p '$soft_threshold_power'
39 -n $plot_genes
40
41
42 ## 2. output report and report site directory
43 -o $wgcna_eigengene_visualization
44 -d $wgcna_eigengene_visualization.files_path
45
46 ## 3. Rmd templates in the tool directory
47
48 -M '${__tool_directory__}/wgcna_eigengene_visualization.Rmd'
49
50
51
52 ]]>
53 </command>
54 <inputs>
55 <param type="data" name="construct_network_workspace" format="rdata" optional="false"
56 label="R workspace from WGCNA: construct network" />
57 <param type="integer" name="soft_threshold_power" optional="true" label="Soft threshold power"
58 help="Refer to the scale independence plot from 'WGCNA: construct network' and choose an optimal soft threshold power.
59 An optimal power will be calculated automatically if no value is provided." />
60 <param type="integer" name="plot_genes" value="400" min="1" label="Number of genes" optional="false"
61 help="The number of genes that will be used. It is possible to speed up the plotting by providing a subset of
62 genes. However, the gene dendrogram may ofter look different from dendrogram of all genes." />
63 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
64 </inputs>
65 <outputs>
66 <data name="wgcna_eigengene_visualization" format="html" label="WGCNA: eigengene visualization" />
67 </outputs>
68 <citations>
69 <citation type="bibtex">
70 @article{langfelder2008wgcna,
71 title={WGCNA: an R package for weighted correlation network analysis},
72 author={Langfelder, Peter and Horvath, Steve},
73 journal={BMC bioinformatics},
74 volume={9},
75 number={1},
76 pages={559},
77 year={2008},
78 publisher={BioMed Central}
79 }
80 </citation>
81 <citation type="bibtex">
82 @article{allaire2016rmarkdown,
83 title={rmarkdown: Dynamic Documents for R, 2016},
84 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
85 journal={R package version 0.9},
86 volume={6},
87 year={2016}
88 }
89 </citation>
90 <citation type="bibtex">
91 @book{xie2015dynamic,
92 title={Dynamic Documents with R and knitr},
93 author={Xie, Yihui},
94 volume={29},
95 year={2015},
96 publisher={CRC Press}
97 }
98 </citation>
99 </citations>
100 </tool>