diff InclusionExclusionListCreator.xml @ 1:b4e991d49651 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

--- a/InclusionExclusionListCreator.xml	Wed Mar 01 12:27:13 2017 -0500
+++ b/InclusionExclusionListCreator.xml	Wed Aug 09 09:12:37 2017 -0400
@@ -1,7 +1,7 @@
 <?xml version='1.0' encoding='UTF-8'?>
 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
 <!--Proposed Tool Section: [Targeted Experiments]-->
-<tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.1.0">
+<tool id="InclusionExclusionListCreator" name="InclusionExclusionListCreator" version="2.2.0">
   <description>Creates inclusion and/or exclusion lists.</description>
   <macros>
     <token name="@EXECUTABLE@">InclusionExclusionListCreator</token>
@@ -39,7 +39,12 @@
   #end for
 #end if
 #if $param_inclusion_strategy:
-  -inclusion_strategy $param_inclusion_strategy
+  -inclusion_strategy
+  #if " " in str($param_inclusion_strategy):
+    "$param_inclusion_strategy"
+  #else
+    $param_inclusion_strategy
+  #end if
 #end if
 
 #if $rep_param_exclusion_charges:
@@ -59,10 +64,20 @@
   -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages
 #end if
 #if $param_algorithm_InclusionExclusionList_RT_unit:
-  -algorithm:InclusionExclusionList:RT:unit $param_algorithm_InclusionExclusionList_RT_unit
+  -algorithm:InclusionExclusionList:RT:unit
+  #if " " in str($param_algorithm_InclusionExclusionList_RT_unit):
+    "$param_algorithm_InclusionExclusionList_RT_unit"
+  #else
+    $param_algorithm_InclusionExclusionList_RT_unit
+  #end if
 #end if
 #if $param_algorithm_InclusionExclusionList_RT_use_relative:
-  -algorithm:InclusionExclusionList:RT:use_relative $param_algorithm_InclusionExclusionList_RT_use_relative
+  -algorithm:InclusionExclusionList:RT:use_relative
+  #if " " in str($param_algorithm_InclusionExclusionList_RT_use_relative):
+    "$param_algorithm_InclusionExclusionList_RT_use_relative"
+  #else
+    $param_algorithm_InclusionExclusionList_RT_use_relative
+  #end if
 #end if
 #if $param_algorithm_InclusionExclusionList_RT_window_relative:
   -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative
@@ -74,7 +89,12 @@
   -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol
 #end if
 #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit:
-  -algorithm:InclusionExclusionList:merge:mz_tol_unit $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
+  -algorithm:InclusionExclusionList:merge:mz_tol_unit
+  #if " " in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit):
+    "$param_algorithm_InclusionExclusionList_merge_mz_tol_unit"
+  #else
+    $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
+  #end if
 #end if
 #if $param_algorithm_InclusionExclusionList_merge_rt_tol:
   -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol
@@ -140,8 +160,8 @@
 #end if
 </command>
   <inputs>
-    <param name="param_include" type="data" format="fasta,featurexml" optional="True" label="Inclusion list input file in FASTA or featureXML format" help="(-include) "/>
-    <param name="param_exclude" type="data" format="fasta,featurexml,idxml" optional="True" label="Exclusion list input file in featureXML, idXML or FASTA format" help="(-exclude) "/>
+    <param name="param_include" type="data" format="featurexml,fasta" optional="True" label="Inclusion list input file in FASTA or featureXML format" help="(-include) "/>
+    <param name="param_exclude" type="data" format="featurexml,idxml,fasta" optional="True" label="Exclusion list input file in featureXML, idXML or FASTA format" help="(-exclude) "/>
     <param name="param_rt_model" type="data" format="txt" optional="True" label="RTModel file used for the rt prediction of peptides in FASTA files" help="(-rt_model) "/>
     <param name="param_pt_model" type="data" format="txt" optional="True" label="PTModel file used for the pt prediction of peptides in FASTA files (only needed for inclusion_strategy PreotinBased_LP)" help="(-pt_model) "/>
     <repeat name="rep_param_inclusion_charges" min="0" max="1" title="param_inclusion_charges">