diff MapAlignerPoseClustering.xml @ 4:e86e83ac0cd3 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

--- a/MapAlignerPoseClustering.xml	Tue Mar 20 14:42:51 2018 -0400
+++ b/MapAlignerPoseClustering.xml	Wed May 15 08:10:13 2019 -0400
@@ -10,7 +10,9 @@
   <expand macro="references"/>
   <expand macro="stdio"/>
   <expand macro="requirements"/>
-  <command><![CDATA[
+  <command detect_errors="aggressive"><![CDATA[
+
+  #import re
 
   mkdir -p ./results_trafoxml ./results_out &&
   MapAlignerPoseClustering
@@ -21,13 +23,15 @@
 #end for
 
 -out
-#for $counter,$infile in enumerate($param_in):
-    ./results_out/${infile.element_identifier}.${infile.extension}
+#for $infile in $param_in:
+  #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier))
+  './results_out/${escaped_element_identifier}.${infile.extension}'
 #end for
 
 -trafo_out
-#for $counter,$infile in enumerate($param_in):
-    ./results_trafoxml/${infile.element_identifier}.trafoxml
+#for $infile in $param_in:
+  #set escaped_element_identifier = re.sub('[^\w\-\s]', '_', str($infile.element_identifier))
+  './results_trafoxml/${escaped_element_identifier}.trafoxml'
 #end for
 
 #if $param_reference_file:
@@ -184,5 +188,5 @@
     </outputs>
     <help>Corrects retention time distortions between maps using a pose clustering approach.
 
-For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help>
+For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapAlignerPoseClustering.html</help>
 </tool>