# HG changeset patch
# User cmonjeau
# Date 1443446495 0
# Node ID 0e0ff9e9c761123ac06c686e70a54582c1afc89a
# Parent  c9e10e0d6c109a3dd817b0853c04849e8d3da08e
fix inputs clean name

diff -r c9e10e0d6c10 -r 0e0ff9e9c761 STACKS_procrad.xml
--- a/STACKS_procrad.xml	Mon Aug 24 15:39:12 2015 +0000
+++ b/STACKS_procrad.xml	Mon Sep 28 13:21:35 2015 +0000
@@ -236,7 +236,7 @@
 <outputs>
 
     <data format="txt" name="output" label="results.log with ${tool.name} on ${on_string}: demultiplexed and cleaned reads" />
-    <data format="txt" name="additional" label="fast(a/q) file with ${tool.name}" hidden="true">
+    <data format="txt" name="additional" label="fasta/fastq file with ${tool.name}" hidden="true">
           <discover_datasets pattern="__designation_and_ext__" directory="galaxy_outputs" visible="true" />
     </data>
     <data format="zip" name="output_archive" label="all_files.zip with ${tool.name} on ${on_string}: demultiplexed and cleaned reads ">
diff -r c9e10e0d6c10 -r 0e0ff9e9c761 stacks.py
--- a/stacks.py	Mon Aug 24 15:39:12 2015 +0000
+++ b/stacks.py	Mon Sep 28 13:21:35 2015 +0000
@@ -35,7 +35,7 @@
 	for line in open(input_config, "r").readlines():
 		if line.strip() != '':
 			extract=line.strip().split("::")
-			tab_files[extract[0].replace(" (", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1]
+			tab_files[extract[0].replace("(", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1]
 
 	# tabfiles[name]-> path
 	return tab_files
@@ -47,12 +47,12 @@
 	for line in open(input_config, "r").readlines():
 		if line.strip() != '':
 			extract=line.strip().split("::")
-			parse_name=re.search("^STACKS.*\((.*\.[ATCG]*\.fq)\)$", extract[0])
+			parse_name=re.search("STACKS.*\((.*\.[ATCG]*).*\)$", extract[0])
 			# rename galaxy name in a short name
 			if parse_name:				
 				extract[0]=parse_name.groups(1)[0]
 
-			tab_files[extract[0].replace(" (", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1]
+			tab_files[extract[0].replace("(", ".").replace(" ", ".").replace(")", "").replace(":", ".").replace("/", ".")]=extract[1]
 			
 	# tabfiles[name]-> path
 	return tab_files