diff PrecursorIonSelector.xml @ 1:828f4c70d584 draft

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

--- a/PrecursorIonSelector.xml	Wed Mar 01 12:20:14 2017 -0500
+++ b/PrecursorIonSelector.xml	Wed Aug 09 09:02:59 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="PrecursorIonSelector" name="PrecursorIonSelector" version="2.1.0">
+<tool id="PrecursorIonSelector" name="PrecursorIonSelector" version="2.2.0">
   <description>PrecursorIonSelector</description>
   <macros>
     <token name="@EXECUTABLE@">PrecursorIonSelector</token>
@@ -63,7 +63,12 @@
   #end for
 #end if
 #if $param_algorithm_type:
-  -algorithm:type $param_algorithm_type
+  -algorithm:type
+  #if " " in str($param_algorithm_type):
+    "$param_algorithm_type"
+  #else
+    $param_algorithm_type
+  #end if
 #end if
 #if $param_algorithm_max_iteration:
   -algorithm:max_iteration $param_algorithm_max_iteration
@@ -120,7 +125,12 @@
   -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3
 #end if
 #if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs:
-  -algorithm:MIPFormulation:combined_ilp:scale_matching_probs $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs
+  -algorithm:MIPFormulation:combined_ilp:scale_matching_probs
+  #if " " in str($param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs):
+    "$param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs"
+  #else
+    $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs
+  #end if
 #end if
 #if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization:
   -algorithm:MIPFormulation:feature_based:no_intensity_normalization
@@ -132,7 +142,12 @@
   -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance
 #end if
 #if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit:
-  -algorithm:Preprocessing:precursor_mass_tolerance_unit $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
+  -algorithm:Preprocessing:precursor_mass_tolerance_unit
+  #if " " in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit):
+    "$param_algorithm_Preprocessing_precursor_mass_tolerance_unit"
+  #else
+    $param_algorithm_Preprocessing_precursor_mass_tolerance_unit
+  #end if
 #end if
 #if $param_algorithm_Preprocessing_preprocessed_db_path:
   -algorithm:Preprocessing:preprocessed_db_path     "$param_algorithm_Preprocessing_preprocessed_db_path"
@@ -175,7 +190,12 @@
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_solver:
-  -solver $adv_opts.param_solver
+  -solver
+  #if " " in str($adv_opts.param_solver):
+    "$adv_opts.param_solver"
+  #else
+    $adv_opts.param_solver
+  #end if
 #end if
     #if $adv_opts.param_force:
   -force