Mercurial > repos > mingchen0919 > rmarkdown_collection_builder
changeset 15:b4adc08beae7 draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 93b036c66fd754a7af459fa80d3f7f143a68477b-dirty
| author | mingchen0919 |
|---|---|
| date | Mon, 25 Sep 2017 16:37:57 -0400 |
| parents | 26718249095f |
| children | c050c7701262 |
| files | collection_list.Rmd collection_list.xml collection_list_render.R |
| diffstat | 3 files changed, 21 insertions(+), 6 deletions(-) [+] |
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--- a/collection_list.Rmd Mon Sep 25 16:24:24 2017 -0400 +++ b/collection_list.Rmd Mon Sep 25 16:37:57 2017 -0400 @@ -20,6 +20,7 @@ str(opt) ``` +# Rename files ```{r 'rename files'} # create directory @@ -37,4 +38,3 @@ paste0('./files_directory/', new_files)) ``` -# End
--- a/collection_list.xml Mon Sep 25 16:24:24 2017 -0400 +++ b/collection_list.xml Mon Sep 25 16:37:57 2017 -0400 @@ -1,7 +1,4 @@ <tool id="rmarkdown_collection_list" name="Collection type: list" version="1.0.0"> - <description> - Create a 'list' dataset collection from a set of files in Galaxy history. - </description> <requirements> <requirement type="package" version="1.15.0.6-0">pandoc</requirement> <requirement type="package" version="1.20.0">r-getopt</requirement> @@ -9,6 +6,23 @@ <requirement type="package" version="0.3.5">r-htmltools</requirement> <requirement type="package" version="0.5.0">r-dplyr</requirement> </requirements> + <description> + Create a 'list' dataset collection from a set of files in Galaxy history. + </description> + <stdio> + <regex match="Execution halted" + source="both" + level="fatal" + description="Execution halted." /> + <regex match="Error in" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + <regex match="Fatal error" + source="both" + level="fatal" + description="An undefined error occured, please check your intput carefully and contact your administrator." /> + </stdio> <command> <![CDATA[ Rscript '${__tool_directory__}/collection_list_render.R'
--- a/collection_list_render.R Mon Sep 25 16:24:24 2017 -0400 +++ b/collection_list_render.R Mon Sep 25 16:37:57 2017 -0400 @@ -34,7 +34,7 @@ spec_list$ECHO = c('echo', 'e', '1', 'character') spec_list$FORMAT = c('format', 'f', '1', 'character') ##--------2. output report and outputs -------------- -spec_list$REPORT = c('report', 'r', '1', 'character') +spec_list$OUTPUT_HTML = c('list_collection_html', 'r', '1', 'character') spec_list$OUTPUT_DIR = c('list_collection_dir', 'd', '1', 'character') ##--------3. Rmd templates in the tool directory ---------- spec_list$LIST_COLLECTION_RMD = c('list_collection_rmd', 't', '1', 'character') @@ -78,6 +78,7 @@ }) #------ 3. render all Rmd files -------- -render('list_collection.Rmd', output_file = opt$report) +render('list_collection.Rmd', output_file = opt$list_collection_html) + #-------4. manipulate outputs -----------------------------