# HG changeset patch
# User mingchen0919
# Date 1506431688 14400
# Node ID fb9d2ec76d305b3fecfcfb93ce433faa3ecb2c5c
# Parent  a660c2aa20d626975c6af5bc6fdc8c620cde5933
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit fcfbe7caa4638f88ab234d0f62119819d06779f0-dirty

diff -r a660c2aa20d6 -r fb9d2ec76d30 collection_list_paired.Rmd
--- a/collection_list_paired.Rmd	Tue Sep 26 08:59:49 2017 -0400
+++ b/collection_list_paired.Rmd	Tue Sep 26 09:14:48 2017 -0400
@@ -41,7 +41,7 @@
 original_files = list.files('./forward_files_directory')
 # create new files names from original file names
 new_files = gsub('\\.dat', '_forward\\.FORMAT', original_files)
-new_files = paste0('input_', 1:length(original_files), '_forward.FORMAT')
+new_files = paste0('input', 1:length(original_files), '_forward.FORMAT')
 new_files
 # rename files
 file.copy(paste0('./forward_files_directory/', original_files),
@@ -61,7 +61,7 @@
 original_files = list.files('./reverse_files_directory')
 # create new files names from original file names
 new_files = gsub('\\.dat', '_reverse\\.FORMAT', original_files)
-new_files = paste0('input_', 1:length(original_files), '_reverse.FORMAT')
+new_files = paste0('input', 1:length(original_files), '_reverse.FORMAT')
 new_files
 # rename files
 file.copy(paste0('./reverse_files_directory/', original_files),
diff -r a660c2aa20d6 -r fb9d2ec76d30 collection_paired.xml
--- a/collection_paired.xml	Tue Sep 26 08:59:49 2017 -0400
+++ b/collection_paired.xml	Tue Sep 26 09:14:48 2017 -0400
@@ -46,8 +46,8 @@
     </inputs>
     <outputs>
         <data format="html" name="report" label="Collection builder (paired collection)" />
-        <collection type="list:paired" name="list_collection">
-            <discover_datasets pattern="(?P&lt;identifier_0&gt;)_(?P&lt;identifier_1&gt;)\.fq" ext="fastqsanger" directory="files_directory"/>
+        <collection type="paired" name="list_collection">
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P<ext>[^\._]+)?" directory="files_directory"/>
         </collection>
     </outputs>
 </tool>
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