# HG changeset patch
# User galaxyp
# Date 1492546018 14400
# Node ID 108f550ea3c44f8e3c6821ef262c7f9c94d05aa8
# Parent  e37289d089901a8c624908c4928500e5eef95be6
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r e37289d08990 -r 108f550ea3c4 HighResPrecursorMassCorrector.xml
--- a/HighResPrecursorMassCorrector.xml	Wed Mar 01 12:55:06 2017 -0500
+++ b/HighResPrecursorMassCorrector.xml	Tue Apr 18 16:06:58 2017 -0400
@@ -28,7 +28,12 @@
   -feature:mz_tolerance $param_feature_mz_tolerance
 #end if
 #if $param_feature_mz_tolerance_unit:
-  -feature:mz_tolerance_unit $param_feature_mz_tolerance_unit
+  -feature:mz_tolerance_unit
+  #if " " in str($param_feature_mz_tolerance_unit):
+    "$param_feature_mz_tolerance_unit"
+  #else
+    $param_feature_mz_tolerance_unit
+  #end if
 #end if
 #if $param_feature_rt_tolerance:
   -feature:rt_tolerance $param_feature_rt_tolerance
@@ -46,7 +51,12 @@
   -nearest_peak:mz_tolerance $param_nearest_peak_mz_tolerance
 #end if
 #if $param_nearest_peak_mz_tolerance_unit:
-  -nearest_peak:mz_tolerance_unit $param_nearest_peak_mz_tolerance_unit
+  -nearest_peak:mz_tolerance_unit
+  #if " " in str($param_nearest_peak_mz_tolerance_unit):
+    "$param_nearest_peak_mz_tolerance_unit"
+  #else
+    $param_nearest_peak_mz_tolerance_unit
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
diff -r e37289d08990 -r 108f550ea3c4 readme.md
--- a/readme.md	Wed Mar 01 12:55:06 2017 -0500
+++ b/readme.md	Tue Apr 18 16:06:58 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.: