# HG changeset patch
# User galaxyp
# Date 1492544978 14400
# Node ID df637a1ed4ca01e6f3d3565b122526aad555007e
# Parent  4e9f2061888d5a297d19993de549ecced9e45c54
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 4e9f2061888d -r df637a1ed4ca ProteinResolver.xml
--- a/ProteinResolver.xml	Wed Mar 01 10:08:31 2017 -0500
+++ b/ProteinResolver.xml	Tue Apr 18 15:49:38 2017 -0400
@@ -44,7 +44,12 @@
   -resolver:min_length $param_resolver_min_length
 #end if
 #if $param_resolver_enzyme:
-  -resolver:enzyme $param_resolver_enzyme
+  -resolver:enzyme
+  #if " " in str($param_resolver_enzyme):
+    "$param_resolver_enzyme"
+  #else
+    $param_resolver_enzyme
+  #end if
 #end if
 #if $param_designer_experiment:
   -designer:experiment     "$param_designer_experiment"
@@ -53,7 +58,12 @@
   -designer:file     "$param_designer_file"
 #end if
 #if $param_designer_separator:
-  -designer:separator $param_designer_separator
+  -designer:separator
+  #if " " in str($param_designer_separator):
+    "$param_designer_separator"
+  #else
+    $param_designer_separator
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
diff -r 4e9f2061888d -r df637a1ed4ca readme.md
--- a/readme.md	Wed Mar 01 10:08:31 2017 -0500
+++ b/readme.md	Tue Apr 18 15:49:38 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.: