# HG changeset patch
# User galaxyp
# Date 1492544858 14400
# Node ID 8d74240aafb9f6bd65e9cfd8cfd76b168d1b2c5b
# Parent  2741adc39601d100985efc717e587470a5885d5a
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 2741adc39601 -r 8d74240aafb9 PeakPickerHiRes.xml
--- a/PeakPickerHiRes.xml	Wed Mar 01 09:58:38 2017 -0500
+++ b/PeakPickerHiRes.xml	Tue Apr 18 15:47:38 2017 -0400
@@ -36,7 +36,12 @@
   -algorithm:report_FWHM
 #end if
 #if $param_algorithm_report_FWHM_unit:
-  -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit"
+  -algorithm:report_FWHM_unit
+  #if " " in str($param_algorithm_report_FWHM_unit):
+    "$param_algorithm_report_FWHM_unit"
+  #else
+    $param_algorithm_report_FWHM_unit
+  #end if
 #end if
 #if $param_algorithm_SignalToNoise_win_len:
   -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len
@@ -48,11 +53,21 @@
   -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements
 #end if
 #if $param_algorithm_SignalToNoise_write_log_messages:
-  -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages
+  -algorithm:SignalToNoise:write_log_messages
+  #if " " in str($param_algorithm_SignalToNoise_write_log_messages):
+    "$param_algorithm_SignalToNoise_write_log_messages"
+  #else
+    $param_algorithm_SignalToNoise_write_log_messages
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_processOption:
-  -processOption $adv_opts.param_processOption
+  -processOption
+  #if " " in str($adv_opts.param_processOption):
+    "$adv_opts.param_processOption"
+  #else
+    $adv_opts.param_processOption
+  #end if
 #end if
     #if $adv_opts.param_force:
   -force
diff -r 2741adc39601 -r 8d74240aafb9 readme.md
--- a/readme.md	Wed Mar 01 09:58:38 2017 -0500
+++ b/readme.md	Tue Apr 18 15:47:38 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.: