# HG changeset patch
# User galaxyp
# Date 1492545178 14400
# Node ID 0ca8724c404a0e569f42a4e2917aaf0e8ef87183
# Parent  2f4218b988057765cd20d785d03ac8b8703b56b4
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 2f4218b98805 -r 0ca8724c404a SimpleSearchEngine.xml
--- a/SimpleSearchEngine.xml	Wed Mar 01 10:10:25 2017 -0500
+++ b/SimpleSearchEngine.xml	Tue Apr 18 15:52:58 2017 -0400
@@ -22,19 +22,34 @@
   -out $param_out
 #end if
 #if $param_enzyme:
-  -enzyme $param_enzyme
+  -enzyme
+  #if " " in str($param_enzyme):
+    "$param_enzyme"
+  #else
+    $param_enzyme
+  #end if
 #end if
 #if $param_precursor_mass_tolerance:
   -precursor:mass_tolerance $param_precursor_mass_tolerance
 #end if
 #if $param_precursor_mass_tolerance_unit:
-  -precursor:mass_tolerance_unit $param_precursor_mass_tolerance_unit
+  -precursor:mass_tolerance_unit
+  #if " " in str($param_precursor_mass_tolerance_unit):
+    "$param_precursor_mass_tolerance_unit"
+  #else
+    $param_precursor_mass_tolerance_unit
+  #end if
 #end if
 #if $param_fragment_mass_tolerance:
   -fragment:mass_tolerance $param_fragment_mass_tolerance
 #end if
 #if $param_fragment_mass_tolerance_unit:
-  -fragment:mass_tolerance_unit $param_fragment_mass_tolerance_unit
+  -fragment:mass_tolerance_unit
+  #if " " in str($param_fragment_mass_tolerance_unit):
+    "$param_fragment_mass_tolerance_unit"
+  #else
+    $param_fragment_mass_tolerance_unit
+  #end if
 #end if
 
 #if $rep_param_modifications_fixed:
diff -r 2f4218b98805 -r 0ca8724c404a readme.md
--- a/readme.md	Wed Mar 01 10:10:25 2017 -0500
+++ b/readme.md	Tue Apr 18 15:52:58 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.: