Mercurial > repos > mingchen0919 > rmarkdown_wgcna

annotate 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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4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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1 <tool id="wgcna_construct_network" name="WGCNA: construct network" version="1.0.0">
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2 <requirements>
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3 <requirement type="package" version="1.20.0">r-getopt</requirement>
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4 <requirement type="package" version="1.2">r-rmarkdown</requirement>
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5 <requirement type="package" version="1.8.4">r-plyr</requirement>
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6 <requirement type="package" version="0.4.0">r-highcharter</requirement>
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7 <requirement type="package" version="0.2">r-dt</requirement>
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8 <requirement type="package" version="0.3.5">r-htmltools</requirement>
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9 <requirement type="package" version="1.51">r-wgcna</requirement>
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10 </requirements>
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11 <description>
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12 Construct gene network.
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13 </description>
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14 <stdio>
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15 <regex match="Execution halted"
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16 source="both"
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17 level="fatal"
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18 description="Execution halted." />
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19 <regex match="Error in"
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20 source="both"
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21 level="fatal"
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22 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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23 <regex match="Fatal error"
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24 source="both"
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25 level="fatal"
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26 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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27 </stdio>
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28 <command>
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29 <![CDATA[
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30
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31 Rscript '${__tool_directory__}/wgcna_construct_network_render.R'
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32
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33 ## 1. input data
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34 -e $echo
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35 -w $preprocessing_workspace
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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36 -h '$height_cut'
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37 -t $trait_data
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38
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39
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40
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41 ## 2. output report and report site directory
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42 -o $wgcna_construct_network
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43 -d $wgcna_construct_network.files_path
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44 -W $construct_network_workspace
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45
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46
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47 ## 3. Rmd templates in the tool directory
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48
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49 ## _site.yml and index.Rmd template files
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50 -M '${__tool_directory__}/wgcna_construct_network.Rmd'
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51
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52
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53
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54 ]]>
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55 </command>
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56 <inputs>
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57 <param type="data" name="preprocessing_workspace" format="rdata" optional="false"
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58 label="R workspace from WGCNA: preprocessing" />
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59 <param type="float" name="height_cut" optional="true" label="Height"
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60 help="Refer to the sample clustering plot from WGCNA: preprocessing and choose a height cut that will
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61 remove outliers. If there is not outlier, leave this field blank." />
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62 <param type="data" name="trait_data" format="csv" optional="true"
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63 label="Trait data"
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64 help="If trait data is provided, a plot consisting of sample clustering and trait heatmap will
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65 be generated. This field is optional. "/>
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66
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67 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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68 </inputs>
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69 <outputs>
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70 <data name="wgcna_construct_network" format="html" label="WGCNA: construct_network" />
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71 <data name="construct_network_workspace" format="rdata" label="R workspace: WGCNA construct_network" />
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72 </outputs>
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73 <citations>
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74 <citation type="bibtex">
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75 @article{langfelder2008wgcna,
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76 title={WGCNA: an R package for weighted correlation network analysis},
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77 author={Langfelder, Peter and Horvath, Steve},
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78 journal={BMC bioinformatics},
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79 volume={9},
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80 number={1},
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81 pages={559},
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82 year={2008},
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83 publisher={BioMed Central}
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84 }
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85 </citation>
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86 <citation type="bibtex">
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87 @article{allaire2016rmarkdown,
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88 title={rmarkdown: Dynamic Documents for R, 2016},
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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},
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90 journal={R package version 0.9},
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91 volume={6},
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92 year={2016}
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93 }
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94 </citation>
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95 <citation type="bibtex">
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96 @book{xie2015dynamic,
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97 title={Dynamic Documents with R and knitr},
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98 author={Xie, Yihui},
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99 volume={29},
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100 year={2015},
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101 publisher={CRC Press}
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102 }
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103 </citation>
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104 </citations>
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105 </tool>