Mercurial > repos > galaxyp > openms_precursorionselector

diff PrecursorIonSelector.xml @ 1:ba0c07f3cb9f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 15:48:45 -0400
parents d53ccfc9c11f
children e2785d77ac17
line wrap: on
line diff
--- a/PrecursorIonSelector.xml	Wed Mar 01 09:57:53 2017 -0500
+++ b/PrecursorIonSelector.xml	Tue Apr 18 15:48:45 2017 -0400
@@ -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