Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

annotate collection_list.Rmd @ 2:f8d0ad99fe9b draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit ec13349788ea42e106b5ba3fc1a5095ed755e644-dirty
author mingchen0919
date Mon, 25 Sep 2017 14:34:53 -0400
parents f85a6bcf940e
children 9c2059916485
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87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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1 ---
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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2 title: 'Collection builder (collection type: list)'
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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3 output:
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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4 html_document:
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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5 number_sections: true
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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6 toc: true
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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7 theme: cosmo
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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8 highlight: tango
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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9 ---
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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10
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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12 knitr::opts_chunk$set(
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
parents:
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13 echo = ECHO
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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14 )
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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15 ```
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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17 ```{r}
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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18 str(opt)
87c21e14f221 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571
mingchen0919
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19 ```
1
f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
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f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
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f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
parents: 0
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22 ```{bash 'copy data to working directory', echo=FALSE}
f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
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23 mkdir files_directory
f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
parents: 0
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24 # Copy uploaded data to the working directory
f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
parents: 0
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25 for f in $(echo FILE_LIST | sed "s/,/ /g")
f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
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26 do
f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
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27 cp $f ./files_directory
f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
parents: 0
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28 done
f85a6bcf940e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fecb83fd1c7b99c3672a61222f3822637eff2571-dirty
mingchen0919
parents: 0
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29 ```