# HG changeset patch
# User galaxyp
# Date 1492544399 14400
# Node ID 55817a7034bead8af12ce0f96ae7dd01ba81529e
# Parent  ea658d0af701c29c9f0ca8b7bea17b4688ffcff1
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r ea658d0af701 -r 55817a7034be LuciphorAdapter.xml
--- a/LuciphorAdapter.xml	Wed Mar 01 10:10:37 2017 -0500
+++ b/LuciphorAdapter.xml	Tue Apr 18 15:39:59 2017 -0400
@@ -22,13 +22,23 @@
   -out $param_out
 #end if
 #if $param_fragment_method:
-  -fragment_method $param_fragment_method
+  -fragment_method
+  #if " " in str($param_fragment_method):
+    "$param_fragment_method"
+  #else
+    $param_fragment_method
+  #end if
 #end if
 #if $param_fragment_mass_tolerance:
   -fragment_mass_tolerance $param_fragment_mass_tolerance
 #end if
 #if $param_fragment_error_units:
-  -fragment_error_units $param_fragment_error_units
+  -fragment_error_units
+  #if " " in str($param_fragment_error_units):
+    "$param_fragment_error_units"
+  #else
+    $param_fragment_error_units
+  #end if
 #end if
 #if $param_min_mz:
   -min_mz $param_min_mz
@@ -91,7 +101,12 @@
   -num_threads $param_num_threads
 #end if
 #if $param_run_mode:
-  -run_mode $param_run_mode
+  -run_mode
+  #if " " in str($param_run_mode):
+    "$param_run_mode"
+  #else
+    $param_run_mode
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
diff -r ea658d0af701 -r 55817a7034be readme.md
--- a/readme.md	Wed Mar 01 10:10:37 2017 -0500
+++ b/readme.md	Tue Apr 18 15:39:59 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.: