# HG changeset patch
# User galaxyp
# Date 1492544925 14400
# Node ID ba0c07f3cb9f5d37a6b4b3d72a9e102c50d5890f
# Parent  d53ccfc9c11fefa3938deccc775d3b2c20b20234
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r d53ccfc9c11f -r ba0c07f3cb9f PrecursorIonSelector.xml
--- 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
diff -r d53ccfc9c11f -r ba0c07f3cb9f readme.md
--- a/readme.md	Wed Mar 01 09:57:53 2017 -0500
+++ b/readme.md	Tue Apr 18 15:48:45 2017 -0400
@@ -39,10 +39,10 @@
  * clone or install CTD2Galaxy
 
     ```bash
-    git clone https://github.com/blankclemens/CTD2Galaxy.git
+    git clone https://github.com/WorkflowConversion/CTD2Galaxy.git
     ```
     
- * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. 
+ * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository.
 
     ```bash
     python generator.py \ 
@@ -102,13 +102,6 @@
     [...]
     ]]>
     ```
- * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line
- 
-        -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit
-     
-   and change it to
-   
-        -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
 
  * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: