# HG changeset patch
# User galaxyp
# Date 1492546062 14400
# Node ID f700da3ba35f61f6c303915074eb0974e6a2f6a1
# Parent  bea4646ed5918af7543cee5a2973ed6ba85edf2d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r bea4646ed591 -r f700da3ba35f IDFileConverter.xml
--- a/IDFileConverter.xml	Wed Mar 01 12:26:05 2017 -0500
+++ b/IDFileConverter.xml	Tue Apr 18 16:07:42 2017 -0400
@@ -36,7 +36,12 @@
   -peptideprophet_analyzed
 #end if
 #if $param_score_type:
-  -score_type $param_score_type
+  -score_type
+  #if " " in str($param_score_type):
+    "$param_score_type"
+  #else
+    $param_score_type
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_ignore_proteins_per_peptide:
diff -r bea4646ed591 -r f700da3ba35f readme.md
--- a/readme.md	Wed Mar 01 12:26:05 2017 -0500
+++ b/readme.md	Tue Apr 18 16:07:42 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.: