# HG changeset patch
# User galaxyp
# Date 1492544898 14400
# Node ID 9b1d75e9e8ca6f40b87ea093070d25f2607e9eb2
# Parent  6be423eab02bc52184e15fb9bad57d6448845ef2
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 6be423eab02b -r 9b1d75e9e8ca PeptideIndexer.xml
--- a/PeptideIndexer.xml	Wed Mar 01 10:14:35 2017 -0500
+++ b/PeptideIndexer.xml	Tue Apr 18 15:48:18 2017 -0400
@@ -25,10 +25,20 @@
   -decoy_string     "$param_decoy_string"
 #end if
 #if $param_decoy_string_position:
-  -decoy_string_position $param_decoy_string_position
+  -decoy_string_position
+  #if " " in str($param_decoy_string_position):
+    "$param_decoy_string_position"
+  #else
+    $param_decoy_string_position
+  #end if
 #end if
 #if $param_missing_decoy_action:
-  -missing_decoy_action $param_missing_decoy_action
+  -missing_decoy_action
+  #if " " in str($param_missing_decoy_action):
+    "$param_missing_decoy_action"
+  #else
+    $param_missing_decoy_action
+  #end if
 #end if
 #if $param_write_protein_sequence:
   -write_protein_sequence
@@ -58,10 +68,20 @@
   -filter_aaa_proteins
 #end if
 #if $param_enzyme_name:
-  -enzyme:name $param_enzyme_name
+  -enzyme:name
+  #if " " in str($param_enzyme_name):
+    "$param_enzyme_name"
+  #else
+    $param_enzyme_name
+  #end if
 #end if
 #if $param_enzyme_specificity:
-  -enzyme:specificity $param_enzyme_specificity
+  -enzyme:specificity
+  #if " " in str($param_enzyme_specificity):
+    "$param_enzyme_specificity"
+  #else
+    $param_enzyme_specificity
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
diff -r 6be423eab02b -r 9b1d75e9e8ca readme.md
--- a/readme.md	Wed Mar 01 10:14:35 2017 -0500
+++ b/readme.md	Tue Apr 18 15:48:18 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.: