# HG changeset patch
# User galaxyp
# Date 1492544504 14400
# Node ID bcb3f7dc36e1e174657a0f87937de36b46f807ba
# Parent  34e4f136ff49f06ce8991f689d705a9f8844c4ac
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 34e4f136ff49 -r bcb3f7dc36e1 MapRTTransformer.xml
--- a/MapRTTransformer.xml	Wed Mar 01 10:00:22 2017 -0500
+++ b/MapRTTransformer.xml	Tue Apr 18 15:41:44 2017 -0400
@@ -31,7 +31,12 @@
   -store_original_rt
 #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_linear_symmetric_regression:
   -model:linear:symmetric_regression
@@ -43,7 +48,12 @@
   -model:b_spline:num_nodes $param_model_b_spline_num_nodes
 #end if
 #if $param_model_b_spline_extrapolate:
-  -model:b_spline:extrapolate $param_model_b_spline_extrapolate
+  -model:b_spline:extrapolate
+  #if " " in str($param_model_b_spline_extrapolate):
+    "$param_model_b_spline_extrapolate"
+  #else
+    $param_model_b_spline_extrapolate
+  #end if
 #end if
 #if $param_model_b_spline_boundary_condition:
   -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
@@ -58,16 +68,36 @@
   -model:lowess:delta $param_model_lowess_delta
 #end if
 #if $param_model_lowess_interpolation_type:
-  -model:lowess:interpolation_type $param_model_lowess_interpolation_type
+  -model:lowess:interpolation_type
+  #if " " in str($param_model_lowess_interpolation_type):
+    "$param_model_lowess_interpolation_type"
+  #else
+    $param_model_lowess_interpolation_type
+  #end if
 #end if
 #if $param_model_lowess_extrapolation_type:
-  -model:lowess:extrapolation_type $param_model_lowess_extrapolation_type
+  -model:lowess:extrapolation_type
+  #if " " in str($param_model_lowess_extrapolation_type):
+    "$param_model_lowess_extrapolation_type"
+  #else
+    $param_model_lowess_extrapolation_type
+  #end if
 #end if
 #if $param_model_interpolated_interpolation_type:
-  -model:interpolated:interpolation_type $param_model_interpolated_interpolation_type
+  -model:interpolated:interpolation_type
+  #if " " in str($param_model_interpolated_interpolation_type):
+    "$param_model_interpolated_interpolation_type"
+  #else
+    $param_model_interpolated_interpolation_type
+  #end if
 #end if
 #if $param_model_interpolated_extrapolation_type:
-  -model:interpolated:extrapolation_type $param_model_interpolated_extrapolation_type
+  -model:interpolated:extrapolation_type
+  #if " " in str($param_model_interpolated_extrapolation_type):
+    "$param_model_interpolated_extrapolation_type"
+  #else
+    $param_model_interpolated_extrapolation_type
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
diff -r 34e4f136ff49 -r bcb3f7dc36e1 readme.md
--- a/readme.md	Wed Mar 01 10:00:22 2017 -0500
+++ b/readme.md	Tue Apr 18 15:41:44 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.: