# HG changeset patch
# User galaxyp
# Date 1492545897 14400
# Node ID 23d1e0b5cf9fcba7e005c70703aeb757d55d1b72
# Parent  14e0f052de8e9d41ff5b79908d716bae9a413b21
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 14e0f052de8e -r 23d1e0b5cf9f FeatureFinderMultiplex.xml
--- a/FeatureFinderMultiplex.xml	Wed Mar 01 12:37:44 2017 -0500
+++ b/FeatureFinderMultiplex.xml	Tue Apr 18 16:04:57 2017 -0400
@@ -40,7 +40,12 @@
   -algorithm:mz_tolerance $param_algorithm_mz_tolerance
 #end if
 #if $param_algorithm_mz_unit:
-  -algorithm:mz_unit $param_algorithm_mz_unit
+  -algorithm:mz_unit
+  #if " " in str($param_algorithm_mz_unit):
+    "$param_algorithm_mz_unit"
+  #else
+    $param_algorithm_mz_unit
+  #end if
 #end if
 #if $param_algorithm_intensity_cutoff:
   -algorithm:intensity_cutoff $param_algorithm_intensity_cutoff
@@ -68,7 +73,12 @@
   -algorithm:knock_out
 #end if
     #if $adv_opts.param_algorithm_averagine_type:
-  -algorithm:averagine_type $adv_opts.param_algorithm_averagine_type
+  -algorithm:averagine_type
+  #if " " in str($adv_opts.param_algorithm_averagine_type):
+    "$adv_opts.param_algorithm_averagine_type"
+  #else
+    $adv_opts.param_algorithm_averagine_type
+  #end if
 #end if
     #if $adv_opts.param_labels_Arg6:
   -labels:Arg6 $adv_opts.param_labels_Arg6
diff -r 14e0f052de8e -r 23d1e0b5cf9f readme.md
--- a/readme.md	Wed Mar 01 12:37:44 2017 -0500
+++ b/readme.md	Tue Apr 18 16:04:57 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.: