# HG changeset patch
# User galaxyp
# Date 1492545698 14400
# Node ID 392ac92169ea654e6986d487e948ef9bb54fb2ed
# Parent  7657ce3b6cee9910d16aa97314945b903a1a1bd9
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 7657ce3b6cee -r 392ac92169ea Decharger.xml
--- a/Decharger.xml	Wed Mar 01 12:41:24 2017 -0500
+++ b/Decharger.xml	Tue Apr 18 16:01:38 2017 -0400
@@ -34,7 +34,12 @@
   -algorithm:FeatureDeconvolution:charge_span_max $param_algorithm_FeatureDeconvolution_charge_span_max
 #end if
 #if $param_algorithm_FeatureDeconvolution_q_try:
-  -algorithm:FeatureDeconvolution:q_try $param_algorithm_FeatureDeconvolution_q_try
+  -algorithm:FeatureDeconvolution:q_try
+  #if " " in str($param_algorithm_FeatureDeconvolution_q_try):
+    "$param_algorithm_FeatureDeconvolution_q_try"
+  #else
+    $param_algorithm_FeatureDeconvolution_q_try
+  #end if
 #end if
 #if $param_algorithm_FeatureDeconvolution_retention_max_diff:
   -algorithm:FeatureDeconvolution:retention_max_diff $param_algorithm_FeatureDeconvolution_retention_max_diff
diff -r 7657ce3b6cee -r 392ac92169ea readme.md
--- a/readme.md	Wed Mar 01 12:41:24 2017 -0500
+++ b/readme.md	Tue Apr 18 16:01:38 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.: