Mercurial > repos > mingchen0919 > rmarkdown_wgcna
annotate wgcna_preprocessing.xml @ 3:240af4b07b92 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author | mingchen0919 |
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date | Tue, 08 Aug 2017 15:06:26 -0400 |
parents | 237210176a2b |
children | a41eb67bce4c |
rev | line source |
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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_preprocessing" name="WGCNA: preprocessing" 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> |
3
240af4b07b92
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
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3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> |
0
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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4 <requirement type="package" version="1.20.0">r-getopt</requirement> |
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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="1.2">r-rmarkdown</requirement> |
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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="1.8.4">r-plyr</requirement> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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7 <requirement type="package" version="0.4.0">r-highcharter</requirement> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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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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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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10 <requirement type="package" version="1.51">r-wgcna</requirement> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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11 </requirements> |
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12 <description> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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13 Data clearning and preprocessing. |
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14 </description> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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15 <stdio> |
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16 <regex match="Execution halted" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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17 source="both" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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18 level="fatal" |
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19 description="Execution halted." /> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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20 <regex match="Error in" |
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21 source="both" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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22 level="fatal" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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23 description="An undefined error occured, please check your intput carefully and contact your administrator." /> |
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 <regex match="Fatal error" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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25 source="both" |
4275479ada3a
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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26 level="fatal" |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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27 description="An undefined error occured, please check your intput carefully and contact your administrator." /> |
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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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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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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_wgcna commit d91f269e8bc09a488ed2e005122bbb4a521f44a0-dirty
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33 |
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34 Rscript '${__tool_directory__}/wgcna_preprocessing_render.R' |
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35 |
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36 ## 1. input data |
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37 -e $echo |
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38 -E $expression_data |
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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_preprocessing |
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43 -d $wgcna_preprocessing.files_path |
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44 -w $preprocessing_workspace |
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45 |
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46 ## 3. Rmd templates sitting in the tool directory |
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47 |
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48 ## _site.yml and index.Rmd template files |
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49 -D '${__tool_directory__}/wgcna_preprocessing.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="expression_data" format="csv" optional="false" label="Gene expression data" |
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57 help="Each row represents a gene and each column represents a sample."/> |
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58 |
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59 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" /> |
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60 </inputs> |
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61 <outputs> |
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62 <data name="wgcna_preprocessing" format="html" label="WGCNA: preprocessing" /> |
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63 <data name="preprocessing_workspace" format="rdata" label="R workspace: WGCNA preprocessing" /> |
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64 </outputs> |
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65 <citations> |
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66 <citation type="bibtex"> |
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67 @article{langfelder2008wgcna, |
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68 title={WGCNA: an R package for weighted correlation network analysis}, |
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69 author={Langfelder, Peter and Horvath, Steve}, |
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70 journal={BMC bioinformatics}, |
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71 volume={9}, |
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72 number={1}, |
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73 pages={559}, |
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74 year={2008}, |
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75 publisher={BioMed Central} |
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76 } |
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77 </citation> |
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78 <citation type="bibtex"> |
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79 @article{allaire2016rmarkdown, |
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80 title={rmarkdown: Dynamic Documents for R, 2016}, |
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81 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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82 journal={R package version 0.9}, |
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83 volume={6}, |
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84 year={2016} |
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85 } |
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86 </citation> |
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87 <citation type="bibtex"> |
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88 @book{xie2015dynamic, |
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89 title={Dynamic Documents with R and knitr}, |
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90 author={Xie, Yihui}, |
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91 volume={29}, |
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92 year={2015}, |
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93 publisher={CRC Press} |
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94 } |
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95 </citation> |
1
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96 <citation> |
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97 @misc{dt2016, |
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98 title = {DT: A Wrapper of the JavaScript Library 'DataTables'}, |
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99 author = {Yihui Xie}, |
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100 year = {2016}, |
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101 note = {R package version 0.2}, |
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102 url = {https://CRAN.R-project.org/package=DT}, |
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103 } |
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104 </citation> |
0
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105 </citations> |
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106 </tool> |