Mercurial > repos > mingchen0919 > rmarkdown_wgcna

annotate wgcna_eigengene_visualization.xml @ 3:240af4b07b92 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author mingchen0919
date Tue, 08 Aug 2017 15:06:26 -0400
parents 237210176a2b
children a41eb67bce4c
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1 <tool id="wgcna_eigengene_visualization" name="WGCNA: eigengene visualization" version="1.0.0">
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2 <requirements>
3
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
0
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4 <requirement type="package" version="1.20.0">r-getopt</requirement>
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5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
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6 <requirement type="package" version="1.8.4">r-plyr</requirement>
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7 <requirement type="package" version="0.4.0">r-highcharter</requirement>
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8 <requirement type="package" version="0.2">r-dt</requirement>
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9 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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10 <requirement type="package" version="1.51">r-wgcna</requirement>
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11 </requirements>
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12 <description>
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13 Eigengene visualization.
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14 </description>
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15 <stdio>
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16 <regex match="Execution halted"
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17 source="both"
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18 level="fatal"
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19 description="Execution halted." />
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20 <regex match="Error in"
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21 source="both"
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22 level="fatal"
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23 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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24 <regex match="Fatal error"
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25 source="both"
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26 level="fatal"
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27 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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28 </stdio>
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29 <command>
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30 <![CDATA[
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31 ## Add tools to PATH
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32 export PATH=/opt/R-3.2.5/bin:\$PATH &&
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33
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34 Rscript '${__tool_directory__}/wgcna_eigengene_visualization_render.R'
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35
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36 ## 1. input data
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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37 -e $echo
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38 -w $construct_network_workspace
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39 -p '$soft_threshold_power'
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40 -n $plot_genes
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41
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42
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43 ## 2. output report and report site directory
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44 -o $wgcna_eigengene_visualization
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45 -d $wgcna_eigengene_visualization.files_path
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46
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47 ## 3. Rmd templates in the tool directory
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48
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49 -M '${__tool_directory__}/wgcna_eigengene_visualization.Rmd'
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50
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51
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52
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53 ]]>
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54 </command>
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55 <inputs>
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56 <param type="data" name="construct_network_workspace" format="rdata" optional="false"
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57 label="R workspace from WGCNA: construct network" />
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58 <param type="integer" name="soft_threshold_power" optional="true" label="Soft threshold power"
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59 help="Refer to the scale independence plot from 'WGCNA: construct network' and choose an optimal soft threshold power.
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60 An optimal power will be calculated automatically if no value is provided." />
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61 <param type="integer" name="plot_genes" value="400" min="1" label="Number of genes" optional="false"
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62 help="The number of genes that will be used. It is possible to speed up the plotting by providing a subset of
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63 genes. However, the gene dendrogram may ofter look different from dendrogram of all genes." />
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64 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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65 </inputs>
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66 <outputs>
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67 <data name="wgcna_eigengene_visualization" format="html" label="WGCNA: eigengene visualization" />
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68 </outputs>
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69 <citations>
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70 <citation type="bibtex">
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71 @article{langfelder2008wgcna,
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72 title={WGCNA: an R package for weighted correlation network analysis},
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73 author={Langfelder, Peter and Horvath, Steve},
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74 journal={BMC bioinformatics},
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75 volume={9},
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76 number={1},
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77 pages={559},
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78 year={2008},
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79 publisher={BioMed Central}
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80 }
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81 </citation>
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82 <citation type="bibtex">
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83 @article{allaire2016rmarkdown,
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84 title={rmarkdown: Dynamic Documents for R, 2016},
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85 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},
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86 journal={R package version 0.9},
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87 volume={6},
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88 year={2016}
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89 }
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90 </citation>
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91 <citation type="bibtex">
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92 @book{xie2015dynamic,
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93 title={Dynamic Documents with R and knitr},
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94 author={Xie, Yihui},
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95 volume={29},
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96 year={2015},
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97 publisher={CRC Press}
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98 }
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99 </citation>
1
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100 <citation>
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101 @misc{dt2016,
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102 title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
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103 author = {Yihui Xie},
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104 year = {2016},
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105 note = {R package version 0.2},
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106 url = {https://CRAN.R-project.org/package=DT},
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107 }
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108 </citation>
0
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109 </citations>
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110 </tool>