# HG changeset patch
# User galaxyp
# Date 1492544306 14400
# Node ID b72178f151985c152edf45d82c95afe106f014af
# Parent  3ef378e4167329184c41b09f1487c0e3427aafb8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 3ef378e41673 -r b72178f15198 InclusionExclusionListCreator.xml
--- a/InclusionExclusionListCreator.xml	Wed Mar 01 10:02:07 2017 -0500
+++ b/InclusionExclusionListCreator.xml	Tue Apr 18 15:38:26 2017 -0400
@@ -39,7 +39,12 @@
   #end for
 #end if
 #if $param_inclusion_strategy:
-  -inclusion_strategy $param_inclusion_strategy
+  -inclusion_strategy
+  #if " " in str($param_inclusion_strategy):
+    "$param_inclusion_strategy"
+  #else
+    $param_inclusion_strategy
+  #end if
 #end if
 
 #if $rep_param_exclusion_charges:
@@ -59,10 +64,20 @@
   -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages
 #end if
 #if $param_algorithm_InclusionExclusionList_RT_unit:
-  -algorithm:InclusionExclusionList:RT:unit $param_algorithm_InclusionExclusionList_RT_unit
+  -algorithm:InclusionExclusionList:RT:unit
+  #if " " in str($param_algorithm_InclusionExclusionList_RT_unit):
+    "$param_algorithm_InclusionExclusionList_RT_unit"
+  #else
+    $param_algorithm_InclusionExclusionList_RT_unit
+  #end if
 #end if
 #if $param_algorithm_InclusionExclusionList_RT_use_relative:
-  -algorithm:InclusionExclusionList:RT:use_relative $param_algorithm_InclusionExclusionList_RT_use_relative
+  -algorithm:InclusionExclusionList:RT:use_relative
+  #if " " in str($param_algorithm_InclusionExclusionList_RT_use_relative):
+    "$param_algorithm_InclusionExclusionList_RT_use_relative"
+  #else
+    $param_algorithm_InclusionExclusionList_RT_use_relative
+  #end if
 #end if
 #if $param_algorithm_InclusionExclusionList_RT_window_relative:
   -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative
@@ -74,7 +89,12 @@
   -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol
 #end if
 #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit:
-  -algorithm:InclusionExclusionList:merge:mz_tol_unit $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
+  -algorithm:InclusionExclusionList:merge:mz_tol_unit
+  #if " " in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit):
+    "$param_algorithm_InclusionExclusionList_merge_mz_tol_unit"
+  #else
+    $param_algorithm_InclusionExclusionList_merge_mz_tol_unit
+  #end if
 #end if
 #if $param_algorithm_InclusionExclusionList_merge_rt_tol:
   -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol
diff -r 3ef378e41673 -r b72178f15198 readme.md
--- a/readme.md	Wed Mar 01 10:02:07 2017 -0500
+++ b/readme.md	Tue Apr 18 15:38:26 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.: