diff collection_list_paired.xml @ 6:a0c8b2b25774 draft

planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db

--- a/collection_list_paired.xml	Tue Sep 26 00:16:09 2017 -0400
+++ b/collection_list_paired.xml	Tue Sep 26 13:33:22 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="rmarkdown_collection_list_paired" name="Collection type: list:paired" version="1.0.0">
+<tool id="rmarkdown_collection_list_paired" name="Collection type (list:paired)" version="1.0.0">
     <requirements>
         <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
         <requirement type="package" version="1.20.0">r-getopt</requirement>
@@ -7,7 +7,7 @@
         <requirement type="package" version="0.5.0">r-dplyr</requirement>
     </requirements>
     <description>
-        Create a 'list:paired' dataset collection from a set of files in Galaxy history.
+        Create a list of paired dataset collection from files in history.
     </description>
     <stdio>
         <regex match="Execution halted"
@@ -40,14 +40,14 @@
     <inputs>
         <param type="data" name="forward_file_list" multiple="true" label="forward inputs"/>
         <param type="data" name="reverse_file_list" multiple="true" label="reverse inputs"/>
-        <param type="text" name="format" label="the format of input files (e.g., fastq, fastqsanger, fasta)"/>
+        <param type="text" name="format" label="the format (extension) of input files (e.g., fastq, fastqsanger, fasta)"/>
 
         <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
     </inputs>
     <outputs>
         <data format="html" name="report" label="Collection builder (list:paired collection)" />
         <collection type="list:paired" name="list_collection">
-            <discover_datasets pattern="__name_and_ext__" directory="files_directory" visible="true"/>
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="files_directory"/>
         </collection>
     </outputs>
 </tool>
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