Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

changeset 4:63e9500cdeec draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 436d91722b309f61890d13d7ed28cd43c79a5c74
author mingchen0919
date Mon, 25 Sep 2017 16:41:49 -0400
parents cb6efa0f0cb6
children 66022ba24ac7
files collection_list.Rmd collection_list.xml collection_list_render.R
diffstat 3 files changed, 20 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/collection_list.Rmd	Mon Sep 25 16:33:54 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 16:41:49 2017 -0400
@@ -20,6 +20,7 @@
 str(opt)
 ```
 
+# Rename files
 
 ```{r 'rename files'}
 # create directory
@@ -37,9 +38,3 @@
           paste0('./files_directory/', new_files))
 ```
 
-# End
-
-```{r 'test'}
-ls()
-```
-
--- a/collection_list.xml	Mon Sep 25 16:33:54 2017 -0400
+++ b/collection_list.xml	Mon Sep 25 16:41:49 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'
@@ -28,7 +42,7 @@
         <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
     </inputs>
     <outputs>
-        <data format="html" name="report" label="fastqc report" />
+        <data format="html" name="report" label="Collection builder report" />
         <collection type="list" name="list_collection">
             <discover_datasets pattern="__name_and_ext__" directory="files_directory" />
         </collection>
--- a/collection_list_render.R	Mon Sep 25 16:33:54 2017 -0400
+++ b/collection_list_render.R	Mon Sep 25 16:41:49 2017 -0400
@@ -79,6 +79,6 @@
 
 #------ 3. render all Rmd files --------
 render('list_collection.Rmd', output_file = opt$list_collection_html)
-cat('test')
+
 
 #-------4. manipulate outputs -----------------------------