Mercurial > repos > mingchen0919 > rmarkdown_wgcna

annotate wgcna_preprocessing.xml @ 6:05bcad4b5b4f draft default tip

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minor fix function missing issue
author mingchen0919
date Sun, 26 Nov 2017 11:04:08 -0500
parents a1a34771304e
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
05bcad4b5b4f minor fix function missing issue
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1 <tool id="wgcna_preprocessing" name="WGCNA: preprocessing" version="1.0.2">
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>
4
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5 <requirement type="package" version="1.3">r-rmarkdown</requirement>
0
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6 <requirement type="package" version="1.8.4">r-plyr</requirement>
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7 <requirement type="package" version="0.2">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 Data clearning and preprocessing.
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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 ## Add tools to PATH
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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_preprocessing_render.R'
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34
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35 ## 1. input data
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36 -e $echo
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37 -E $expression_data
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38
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39
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40 ## 2. output report and report site directory
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41 -o $wgcna_preprocessing
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42 -d $wgcna_preprocessing.files_path
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43 -w $preprocessing_workspace
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44
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45 ## 3. Rmd templates sitting in the tool directory
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46
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47 ## _site.yml and index.Rmd template files
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48 -D '${__tool_directory__}/wgcna_preprocessing.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="expression_data" format="csv" optional="false" label="Gene expression data"
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56 help="Each row represents a gene and each column represents a sample."/>
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57 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
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58 </inputs>
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59 <outputs>
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60 <data name="wgcna_preprocessing" format="html" label="WGCNA: preprocessing" />
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61 <data name="preprocessing_workspace" format="rdata" label="R workspace: WGCNA preprocessing" />
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62 </outputs>
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63 <citations>
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64 <citation type="bibtex">
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65 @article{langfelder2008wgcna,
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66 title={WGCNA: an R package for weighted correlation network analysis},
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67 author={Langfelder, Peter and Horvath, Steve},
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68 journal={BMC bioinformatics},
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69 volume={9},
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70 number={1},
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71 pages={559},
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72 year={2008},
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73 publisher={BioMed Central}
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74 }
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75 </citation>
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76 <citation type="bibtex">
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77 @article{allaire2016rmarkdown,
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78 title={rmarkdown: Dynamic Documents for R, 2016},
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79 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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80 journal={R package version 0.9},
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81 volume={6},
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82 year={2016}
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83 }
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84 </citation>
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85 <citation type="bibtex">
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86 @book{xie2015dynamic,
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87 title={Dynamic Documents with R and knitr},
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88 author={Xie, Yihui},
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89 volume={29},
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90 year={2015},
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91 publisher={CRC Press}
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92 }
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93 </citation>
1
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94 <citation>
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95 @misc{dt2016,
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96 title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
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97 author = {Yihui Xie},
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98 year = {2016},
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99 note = {R package version 0.2},
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100 url = {https://CRAN.R-project.org/package=DT},
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101 }
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102 </citation>
0
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103 </citations>
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104 </tool>