# HG changeset patch
# User galaxyp
# Date 1492544544 14400
# Node ID 2e48052e1b95939fcfe35a3ab546e5ec6d59fb83
# Parent  8746354dd6a9914f1347c0a658bfde75642da46c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 8746354dd6a9 -r 2e48052e1b95 MascotAdapterOnline.xml
--- a/MascotAdapterOnline.xml	Wed Mar 01 10:18:37 2017 -0500
+++ b/MascotAdapterOnline.xml	Tue Apr 18 15:42:24 2017 -0400
@@ -34,13 +34,23 @@
   -Mascot_parameters:precursor_mass_tolerance $param_Mascot_parameters_precursor_mass_tolerance
 #end if
 #if $param_Mascot_parameters_precursor_error_units:
-  -Mascot_parameters:precursor_error_units $param_Mascot_parameters_precursor_error_units
+  -Mascot_parameters:precursor_error_units
+  #if " " in str($param_Mascot_parameters_precursor_error_units):
+    "$param_Mascot_parameters_precursor_error_units"
+  #else
+    $param_Mascot_parameters_precursor_error_units
+  #end if
 #end if
 #if $param_Mascot_parameters_fragment_mass_tolerance:
   -Mascot_parameters:fragment_mass_tolerance $param_Mascot_parameters_fragment_mass_tolerance
 #end if
 #if $param_Mascot_parameters_fragment_error_units:
-  -Mascot_parameters:fragment_error_units $param_Mascot_parameters_fragment_error_units
+  -Mascot_parameters:fragment_error_units
+  #if " " in str($param_Mascot_parameters_fragment_error_units):
+    "$param_Mascot_parameters_fragment_error_units"
+  #else
+    $param_Mascot_parameters_fragment_error_units
+  #end if
 #end if
 #if $param_Mascot_parameters_charges:
   -Mascot_parameters:charges     "$param_Mascot_parameters_charges"
@@ -71,7 +81,12 @@
   #end for
 #end if
 #if $param_Mascot_parameters_mass_type:
-  -Mascot_parameters:mass_type $param_Mascot_parameters_mass_type
+  -Mascot_parameters:mass_type
+  #if " " in str($param_Mascot_parameters_mass_type):
+    "$param_Mascot_parameters_mass_type"
+  #else
+    $param_Mascot_parameters_mass_type
+  #end if
 #end if
 #if $param_Mascot_parameters_number_of_hits:
   -Mascot_parameters:number_of_hits $param_Mascot_parameters_number_of_hits
@@ -114,7 +129,12 @@
   -force
 #end if
     #if $adv_opts.param_Mascot_parameters_search_type:
-  -Mascot_parameters:search_type $adv_opts.param_Mascot_parameters_search_type
+  -Mascot_parameters:search_type
+  #if " " in str($adv_opts.param_Mascot_parameters_search_type):
+    "$adv_opts.param_Mascot_parameters_search_type"
+  #else
+    $adv_opts.param_Mascot_parameters_search_type
+  #end if
 #end if
     #if $adv_opts.param_Mascot_parameters_special_modifications:
   -Mascot_parameters:special_modifications     "$adv_opts.param_Mascot_parameters_special_modifications"
diff -r 8746354dd6a9 -r 2e48052e1b95 readme.md
--- a/readme.md	Wed Mar 01 10:18:37 2017 -0500
+++ b/readme.md	Tue Apr 18 15:42:24 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.: