Mercurial > repos > mingchen0919 > rmarkdown_wgcna

annotate wgcna_construct_network.xml @ 2:237210176a2b 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 14:33:59 -0400
parents 337fedd38522
children 240af4b07b92
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1 <tool id="wgcna_construct_network" name="WGCNA: construct network" version="1.0.0">
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2 <requirements>
2
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3 <requirement type="package" version="1.19.2.1">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 Construct gene network.
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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
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32 Rscript '${__tool_directory__}/wgcna_construct_network_render.R'
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33
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34 ## 1. input data
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35 -e $echo
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36 -w $preprocessing_workspace
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37 -h '$height_cut'
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38 -t $trait_data
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39
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41
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42 ## 2. output report and report site directory
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43 -o $wgcna_construct_network
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44 -d $wgcna_construct_network.files_path
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45 -W $construct_network_workspace
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46
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47
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48 ## 3. Rmd templates in the tool directory
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49
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50 ## _site.yml and index.Rmd template files
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51 -M '${__tool_directory__}/wgcna_construct_network.Rmd'
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52
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53
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54
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55 ]]>
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56 </command>
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57 <inputs>
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58 <param type="data" name="preprocessing_workspace" format="rdata" optional="false"
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59 label="R workspace from WGCNA: preprocessing" />
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60 <param type="float" name="height_cut" optional="true" label="Height"
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61 help="Refer to the sample clustering plot from WGCNA: preprocessing and choose a height cut that will
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62 remove outliers. If there is not outlier, leave this field blank." />
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63 <param type="data" name="trait_data" format="csv" optional="true"
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64 label="Trait data"
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65 help="If trait data is provided, a plot consisting of sample clustering and trait heatmap will
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66 be generated. This field is optional. "/>
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67
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68 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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69 </inputs>
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70 <outputs>
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71 <data name="wgcna_construct_network" format="html" label="WGCNA: construct_network" />
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72 <data name="construct_network_workspace" format="rdata" label="R workspace: WGCNA construct_network" />
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73 </outputs>
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74 <citations>
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75 <citation type="bibtex">
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76 @article{langfelder2008wgcna,
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77 title={WGCNA: an R package for weighted correlation network analysis},
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78 author={Langfelder, Peter and Horvath, Steve},
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79 journal={BMC bioinformatics},
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80 volume={9},
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81 number={1},
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82 pages={559},
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83 year={2008},
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84 publisher={BioMed Central}
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85 }
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86 </citation>
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87 <citation type="bibtex">
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88 @article{allaire2016rmarkdown,
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89 title={rmarkdown: Dynamic Documents for R, 2016},
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90 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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91 journal={R package version 0.9},
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92 volume={6},
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93 year={2016}
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94 }
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95 </citation>
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96 <citation type="bibtex">
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97 @book{xie2015dynamic,
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98 title={Dynamic Documents with R and knitr},
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99 author={Xie, Yihui},
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100 volume={29},
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101 year={2015},
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102 publisher={CRC Press}
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103 }
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104 </citation>
1
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105 <citation>
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106 @misc{dt2016,
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107 title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
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108 author = {Yihui Xie},
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109 year = {2016},
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110 note = {R package version 0.2},
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111 url = {https://CRAN.R-project.org/package=DT},
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112 }
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113 </citation>
0
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114 </citations>
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115 </tool>