# HG changeset patch
# User galaxyp
# Date 1492544699 14400
# Node ID 617cdb4ca4407cf3eff6d7016f57f1b675507b7e
# Parent  96f5d72528864672635fdacf434a6cbe0e2b3ea9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 96f5d7252886 -r 617cdb4ca440 OpenSwathChromatogramExtractor.xml
--- a/OpenSwathChromatogramExtractor.xml	Wed Mar 01 10:11:51 2017 -0500
+++ b/OpenSwathChromatogramExtractor.xml	Tue Apr 18 15:44:59 2017 -0400
@@ -44,10 +44,20 @@
   -extract_MS1
 #end if
 #if $param_extraction_function:
-  -extraction_function $param_extraction_function
+  -extraction_function
+  #if " " in str($param_extraction_function):
+    "$param_extraction_function"
+  #else
+    $param_extraction_function
+  #end if
 #end if
 #if $param_model_type:
-  -model:type $param_model_type
+  -model:type
+  #if " " in str($param_model_type):
+    "$param_model_type"
+  #else
+    $param_model_type
+  #end if
 #end if
 #if $param_model_symmetric_regression:
   -model:symmetric_regression
diff -r 96f5d7252886 -r 617cdb4ca440 readme.md
--- a/readme.md	Wed Mar 01 10:11:51 2017 -0500
+++ b/readme.md	Tue Apr 18 15:44:59 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.: