Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

annotate collection_paired.Rmd @ 48:68da32dbc6e2 draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit a7ad932a1725b4ef26d522040c5395ae0026fb35-dirty
author mingchen0919
date Tue, 26 Sep 2017 12:34:02 -0400
parents 8dacd341b8b7
children
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335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
1 ---
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
2 title: 'Build collection: a paired datasets'
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
3 output:
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
4 html_document:
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
5 number_sections: true
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
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6 toc: true
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
7 theme: cosmo
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
8 highlight: tango
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
9 ---
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
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335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE}
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
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12 knitr::opts_chunk$set(
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
13 echo = ECHO
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
14 )
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
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15 ```
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
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335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
17 # Command line arguments
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
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335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
19 ```{r 'command line arguments'}
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
20 str(opt)
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
21 ```
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
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335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
23 # Rename files
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
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335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
25 ```{r}
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8dacd341b8b7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 45
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26 file.copy("FORWARD_INPUT", './OUTPUT_DIR/forward.FORMAT')
8dacd341b8b7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 45
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27 file.copy("REVERSE_INPUT", './OUTPUT_DIR/reverse.FORMAT')
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335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
diff changeset
28 ```
335e9eb25532 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit b15eec6b208c8a41b8ad8969ab9c6046d7f0b73c-dirty
mingchen0919
parents: 38
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