# HG changeset patch
# User galaxyp
# Date 1492544438 14400
# Node ID 96c52704abcd99168ce5ef074d2710f61c94a440
# Parent  006142eda968db6b998558a045f6d1ff611d9684
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 006142eda968 -r 96c52704abcd MRMTransitionGroupPicker.xml
--- a/MRMTransitionGroupPicker.xml	Wed Mar 01 10:08:42 2017 -0500
+++ b/MRMTransitionGroupPicker.xml	Tue Apr 18 15:40:38 2017 -0400
@@ -36,7 +36,12 @@
   -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width
 #end if
 #if $param_algorithm_PeakPickerMRM_use_gauss:
-  -algorithm:PeakPickerMRM:use_gauss $param_algorithm_PeakPickerMRM_use_gauss
+  -algorithm:PeakPickerMRM:use_gauss
+  #if " " in str($param_algorithm_PeakPickerMRM_use_gauss):
+    "$param_algorithm_PeakPickerMRM_use_gauss"
+  #else
+    $param_algorithm_PeakPickerMRM_use_gauss
+  #end if
 #end if
 #if $param_algorithm_PeakPickerMRM_peak_width:
   -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width
@@ -51,13 +56,23 @@
   -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count
 #end if
 #if $param_algorithm_PeakPickerMRM_write_sn_log_messages:
-  -algorithm:PeakPickerMRM:write_sn_log_messages $param_algorithm_PeakPickerMRM_write_sn_log_messages
+  -algorithm:PeakPickerMRM:write_sn_log_messages
+  #if " " in str($param_algorithm_PeakPickerMRM_write_sn_log_messages):
+    "$param_algorithm_PeakPickerMRM_write_sn_log_messages"
+  #else
+    $param_algorithm_PeakPickerMRM_write_sn_log_messages
+  #end if
 #end if
 #if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks:
   -algorithm:PeakPickerMRM:remove_overlapping_peaks
 #end if
 #if $param_algorithm_PeakPickerMRM_method:
-  -algorithm:PeakPickerMRM:method $param_algorithm_PeakPickerMRM_method
+  -algorithm:PeakPickerMRM:method
+  #if " " in str($param_algorithm_PeakPickerMRM_method):
+    "$param_algorithm_PeakPickerMRM_method"
+  #else
+    $param_algorithm_PeakPickerMRM_method
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -67,7 +82,12 @@
   -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width
 #end if
     #if $adv_opts.param_algorithm_background_subtraction:
-  -algorithm:background_subtraction $adv_opts.param_algorithm_background_subtraction
+  -algorithm:background_subtraction
+  #if " " in str($adv_opts.param_algorithm_background_subtraction):
+    "$adv_opts.param_algorithm_background_subtraction"
+  #else
+    $adv_opts.param_algorithm_background_subtraction
+  #end if
 #end if
     #if $adv_opts.param_algorithm_recalculate_peaks:
   -algorithm:recalculate_peaks     "$adv_opts.param_algorithm_recalculate_peaks"
diff -r 006142eda968 -r 96c52704abcd readme.md
--- a/readme.md	Wed Mar 01 10:08:42 2017 -0500
+++ b/readme.md	Tue Apr 18 15:40:38 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.: