Mercurial > repos > mingchen0919 > rmarkdown_wgcna

annotate 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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children 337fedd38522
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4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
mingchen0919
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1 <tool id="wgcna_eigengene_visualization" name="WGCNA: eigengene visualization" version="1.0.0">
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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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>
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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5 <requirement type="package" version="1.8.4">r-plyr</requirement>
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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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 Eigengene visualization.
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13 </description>
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14 <stdio>
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15 <regex match="Execution halted"
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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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"
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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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[
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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30 ## Add tools to PATH
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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31 export PATH=/opt/R-3.2.5/bin:\$PATH &&
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32
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33 Rscript '${__tool_directory__}/wgcna_eigengene_visualization_render.R'
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34
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35 ## 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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36 -e $echo
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 -w $construct_network_workspace
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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38 -p '$soft_threshold_power'
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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39 -n $plot_genes
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40
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41
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42 ## 2. output report and report site directory
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43 -o $wgcna_eigengene_visualization
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44 -d $wgcna_eigengene_visualization.files_path
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45
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46 ## 3. Rmd templates in the tool directory
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47
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48 -M '${__tool_directory__}/wgcna_eigengene_visualization.Rmd'
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49
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50
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51
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52 ]]>
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53 </command>
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54 <inputs>
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55 <param type="data" name="construct_network_workspace" format="rdata" optional="false"
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56 label="R workspace from WGCNA: construct network" />
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57 <param type="integer" name="soft_threshold_power" optional="true" label="Soft threshold power"
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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58 help="Refer to the scale independence plot from 'WGCNA: construct network' and choose an optimal soft threshold power.
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59 An optimal power will be calculated automatically if no value is provided." />
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60 <param type="integer" name="plot_genes" value="400" min="1" label="Number of genes" optional="false"
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61 help="The number of genes that will be used. It is possible to speed up the plotting by providing a subset of
4275479ada3a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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62 genes. However, the gene dendrogram may ofter look different from dendrogram of all genes." />
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63 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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64 </inputs>
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65 <outputs>
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66 <data name="wgcna_eigengene_visualization" format="html" label="WGCNA: eigengene visualization" />
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67 </outputs>
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68 <citations>
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69 <citation type="bibtex">
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70 @article{langfelder2008wgcna,
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71 title={WGCNA: an R package for weighted correlation network analysis},
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72 author={Langfelder, Peter and Horvath, Steve},
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73 journal={BMC bioinformatics},
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74 volume={9},
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75 number={1},
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76 pages={559},
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77 year={2008},
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78 publisher={BioMed Central}
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79 }
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80 </citation>
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81 <citation type="bibtex">
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82 @article{allaire2016rmarkdown,
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83 title={rmarkdown: Dynamic Documents for R, 2016},
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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},
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85 journal={R package version 0.9},
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86 volume={6},
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87 year={2016}
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88 }
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89 </citation>
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90 <citation type="bibtex">
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91 @book{xie2015dynamic,
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92 title={Dynamic Documents with R and knitr},
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93 author={Xie, Yihui},
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94 volume={29},
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95 year={2015},
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96 publisher={CRC Press}
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97 }
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98 </citation>
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99 </citations>
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100 </tool>