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comparison wgcna_preprocessing.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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children 337fedd38522
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-1:000000000000 0:4275479ada3a
1 <tool id="wgcna_preprocessing" name="WGCNA: preprocessing" 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 Data clearning and preprocessing.
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_preprocessing_render.R'
34
35 ## 1. input data
36 -e $echo
37 -E $expression_data
38
39
40 ## 2. output report and report site directory
41 -o $wgcna_preprocessing
42 -d $wgcna_preprocessing.files_path
43 -w $preprocessing_workspace
44
45 ## 3. Rmd templates sitting in the tool directory
46
47 ## _site.yml and index.Rmd template files
48 -D '${__tool_directory__}/wgcna_preprocessing.Rmd'
49
50
51
52 ]]>
53 </command>
54 <inputs>
55 <param type="data" name="expression_data" format="csv" optional="false" label="Gene expression data"
56 help="Each row represents a gene and each column represents a sample."/>
57
58 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
59 </inputs>
60 <outputs>
61 <data name="wgcna_preprocessing" format="html" label="WGCNA: preprocessing" />
62 <data name="preprocessing_workspace" format="rdata" label="R workspace: WGCNA preprocessing" />
63 </outputs>
64 <citations>
65 <citation type="bibtex">
66 @article{langfelder2008wgcna,
67 title={WGCNA: an R package for weighted correlation network analysis},
68 author={Langfelder, Peter and Horvath, Steve},
69 journal={BMC bioinformatics},
70 volume={9},
71 number={1},
72 pages={559},
73 year={2008},
74 publisher={BioMed Central}
75 }
76 </citation>
77 <citation type="bibtex">
78 @article{allaire2016rmarkdown,
79 title={rmarkdown: Dynamic Documents for R, 2016},
80 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},
81 journal={R package version 0.9},
82 volume={6},
83 year={2016}
84 }
85 </citation>
86 <citation type="bibtex">
87 @book{xie2015dynamic,
88 title={Dynamic Documents with R and knitr},
89 author={Xie, Yihui},
90 volume={29},
91 year={2015},
92 publisher={CRC Press}
93 }
94 </citation>
95 </citations>
96 </tool>