# HG changeset patch
# User galaxyp
# Date 1492545844 14400
# Node ID 6a3bbd5b8cb65a12ba07b0f93f7bad7d49313911
# Parent  3a61c78033f0f54749a6b3d42901bcbdf15087ad
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 3a61c78033f0 -r 6a3bbd5b8cb6 FeatureFinderIdentification.xml
--- a/FeatureFinderIdentification.xml	Wed Mar 01 12:55:55 2017 -0500
+++ b/FeatureFinderIdentification.xml	Tue Apr 18 16:04:04 2017 -0400
@@ -31,7 +31,12 @@
   -trafo_out $param_trafo_out
 #end if
 #if $param_extract_reference_rt:
-  -extract:reference_rt $param_extract_reference_rt
+  -extract:reference_rt
+  #if " " in str($param_extract_reference_rt):
+    "$param_extract_reference_rt"
+  #else
+    $param_extract_reference_rt
+  #end if
 #end if
 #if $param_extract_rt_window:
   -extract:rt_window $param_extract_rt_window
@@ -46,7 +51,12 @@
   -detect:peak_width $param_detect_peak_width
 #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 $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
diff -r 3a61c78033f0 -r 6a3bbd5b8cb6 readme.md
--- a/readme.md	Wed Mar 01 12:55:55 2017 -0500
+++ b/readme.md	Tue Apr 18 16:04:04 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.: