Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

changeset 10:6afe8433106c draft

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planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 6df7b8ef3a603f7792ed5815ff324ede8a7b2b0b-dirty
author mingchen0919
date Mon, 25 Sep 2017 15:44:25 -0400
parents 9cf2069b31c0
children e2a0bc241b56
files collection_list.Rmd collection_list.xml
diffstat 2 files changed, 3 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/collection_list.Rmd	Mon Sep 25 15:39:35 2017 -0400
+++ b/collection_list.Rmd	Mon Sep 25 15:44:25 2017 -0400
@@ -26,6 +26,6 @@
 # Copy uploaded data to the working directory
 for f in $(echo FILE_LIST | sed "s/,/ /g")
 do
-    cp $f ./files_directory
+    cp $f ./files_directory/$f.fastqsanger
 done
-```
\ No newline at end of file
+```
--- a/collection_list.xml	Mon Sep 25 15:39:35 2017 -0400
+++ b/collection_list.xml	Mon Sep 25 15:44:25 2017 -0400
@@ -28,7 +28,7 @@
     <outputs>
         <data format="html" name="report" label="fastqc report" />
         <collection type="list" name="list_collection">
-            <discover_datasets pattern="__name_and_ext__" format="fastqsanger" directory="files_directory" />
+            <discover_datasets pattern="__name_and_ext__" directory="files_directory" />
         </collection>
     </outputs>
 </tool>
\ No newline at end of file