# HG changeset patch
# User galaxyp
# Date 1492544582 14400
# Node ID 5fc08238d0ce6a5c8d49342741fc97e6143f1cbb
# Parent  0283517872f8d40dcc561d536bbabca556d7794c
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 0283517872f8 -r 5fc08238d0ce MetaProSIP.xml
--- a/MetaProSIP.xml	Wed Mar 01 10:09:33 2017 -0500
+++ b/MetaProSIP.xml	Tue Apr 18 15:43:02 2017 -0400
@@ -52,13 +52,23 @@
   -weight_merge_window $param_weight_merge_window
 #end if
 #if $param_plot_extension:
-  -plot_extension $param_plot_extension
+  -plot_extension
+  #if " " in str($param_plot_extension):
+    "$param_plot_extension"
+  #else
+    $param_plot_extension
+  #end if
 #end if
 #if $param_qc_output_directory:
   -qc_output_directory     "$param_qc_output_directory"
 #end if
 #if $param_labeling_element:
-  -labeling_element $param_labeling_element
+  -labeling_element
+  #if " " in str($param_labeling_element):
+    "$param_labeling_element"
+  #else
+    $param_labeling_element
+  #end if
 #end if
 #if $param_use_unassigned_ids:
   -use_unassigned_ids
@@ -104,7 +114,12 @@
   -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min
 #end if
     #if $adv_opts.param_collect_method:
-  -collect_method $adv_opts.param_collect_method
+  -collect_method
+  #if " " in str($adv_opts.param_collect_method):
+    "$adv_opts.param_collect_method"
+  #else
+    $adv_opts.param_collect_method
+  #end if
 #end if
     #if $adv_opts.param_lowRIA_correlation_threshold:
   -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
diff -r 0283517872f8 -r 5fc08238d0ce readme.md
--- a/readme.md	Wed Mar 01 10:09:33 2017 -0500
+++ b/readme.md	Tue Apr 18 15:43:02 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.: