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comparison wgcna_construct_network.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_construct_network" name="WGCNA: construct network" 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 Construct gene network.
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
31 Rscript '${__tool_directory__}/wgcna_construct_network_render.R'
32
33 ## 1. input data
34 -e $echo
35 -w $preprocessing_workspace
36 -h '$height_cut'
37 -t $trait_data
38
39
40
41 ## 2. output report and report site directory
42 -o $wgcna_construct_network
43 -d $wgcna_construct_network.files_path
44 -W $construct_network_workspace
45
46
47 ## 3. Rmd templates in the tool directory
48
49 ## _site.yml and index.Rmd template files
50 -M '${__tool_directory__}/wgcna_construct_network.Rmd'
51
52
53
54 ]]>
55 </command>
56 <inputs>
57 <param type="data" name="preprocessing_workspace" format="rdata" optional="false"
58 label="R workspace from WGCNA: preprocessing" />
59 <param type="float" name="height_cut" optional="true" label="Height"
60 help="Refer to the sample clustering plot from WGCNA: preprocessing and choose a height cut that will
61 remove outliers. If there is not outlier, leave this field blank." />
62 <param type="data" name="trait_data" format="csv" optional="true"
63 label="Trait data"
64 help="If trait data is provided, a plot consisting of sample clustering and trait heatmap will
65 be generated. This field is optional. "/>
66
67 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
68 </inputs>
69 <outputs>
70 <data name="wgcna_construct_network" format="html" label="WGCNA: construct_network" />
71 <data name="construct_network_workspace" format="rdata" label="R workspace: WGCNA construct_network" />
72 </outputs>
73 <citations>
74 <citation type="bibtex">
75 @article{langfelder2008wgcna,
76 title={WGCNA: an R package for weighted correlation network analysis},
77 author={Langfelder, Peter and Horvath, Steve},
78 journal={BMC bioinformatics},
79 volume={9},
80 number={1},
81 pages={559},
82 year={2008},
83 publisher={BioMed Central}
84 }
85 </citation>
86 <citation type="bibtex">
87 @article{allaire2016rmarkdown,
88 title={rmarkdown: Dynamic Documents for R, 2016},
89 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},
90 journal={R package version 0.9},
91 volume={6},
92 year={2016}
93 }
94 </citation>
95 <citation type="bibtex">
96 @book{xie2015dynamic,
97 title={Dynamic Documents with R and knitr},
98 author={Xie, Yihui},
99 volume={29},
100 year={2015},
101 publisher={CRC Press}
102 }
103 </citation>
104 </citations>
105 </tool>