# HG changeset patch
# User galaxyp
# Date 1492544530 14400
# Node ID 62b5e00c749398c8d1084cc5883890ba70784d7e
# Parent  33ec38d312558c302dbd45426171f7ab6ffa00c9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 33ec38d31255 -r 62b5e00c7493 MascotAdapter.xml
--- a/MascotAdapter.xml	Wed Mar 01 10:06:44 2017 -0500
+++ b/MascotAdapter.xml	Tue Apr 18 15:42:10 2017 -0400
@@ -34,7 +34,12 @@
   -peak_mass_tolerance $param_peak_mass_tolerance
 #end if
 #if $param_taxonomy:
-  -taxonomy $param_taxonomy
+  -taxonomy
+  #if " " in str($param_taxonomy):
+    "$param_taxonomy"
+  #else
+    $param_taxonomy
+  #end if
 #end if
 
 #if $rep_param_modifications:
@@ -76,7 +81,12 @@
   -hits     "$param_hits"
 #end if
 #if $param_cleavage:
-  -cleavage $param_cleavage
+  -cleavage
+  #if " " in str($param_cleavage):
+    "$param_cleavage"
+  #else
+    $param_cleavage
+  #end if
 #end if
 #if $param_missed_cleavages:
   -missed_cleavages $param_missed_cleavages
@@ -112,7 +122,12 @@
   -boundary     "$param_boundary"
 #end if
 #if $param_mass_type:
-  -mass_type $param_mass_type
+  -mass_type
+  #if " " in str($param_mass_type):
+    "$param_mass_type"
+  #else
+    $param_mass_type
+  #end if
 #end if
 #if $param_mascot_directory:
   -mascot_directory     "$param_mascot_directory"
diff -r 33ec38d31255 -r 62b5e00c7493 readme.md
--- a/readme.md	Wed Mar 01 10:06:44 2017 -0500
+++ b/readme.md	Tue Apr 18 15:42:10 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.: