# HG changeset patch
# User galaxyp
# Date 1492545347 14400
# Node ID 773e6b46489a82d51b99f5a6c308fe9a05e1cb9f
# Parent  2b16375066739fa8b945a161ac681a27a96e8118
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 2b1637506673 -r 773e6b46489a SvmTheoreticalSpectrumGeneratorTrainer.xml
--- a/SvmTheoreticalSpectrumGeneratorTrainer.xml	Wed Mar 01 10:06:57 2017 -0500
+++ b/SvmTheoreticalSpectrumGeneratorTrainer.xml	Tue Apr 18 15:55:47 2017 -0400
@@ -40,10 +40,20 @@
   -algorithm:peak_tolerance $param_algorithm_peak_tolerance
 #end if
 #if $param_algorithm_add_b_ions:
-  -algorithm:add_b_ions $param_algorithm_add_b_ions
+  -algorithm:add_b_ions
+  #if " " in str($param_algorithm_add_b_ions):
+    "$param_algorithm_add_b_ions"
+  #else
+    $param_algorithm_add_b_ions
+  #end if
 #end if
 #if $param_algorithm_add_y_ions:
-  -algorithm:add_y_ions $param_algorithm_add_y_ions
+  -algorithm:add_y_ions
+  #if " " in str($param_algorithm_add_y_ions):
+    "$param_algorithm_add_y_ions"
+  #else
+    $param_algorithm_add_y_ions
+  #end if
 #end if
 #if $param_algorithm_add_a_ions:
   -algorithm:add_a_ions
@@ -73,7 +83,12 @@
   -algorithm:svm:svr_type $param_algorithm_svm_svr_type
 #end if
 #if $param_algorithm_svm_scaling:
-  -algorithm:svm:scaling $param_algorithm_svm_scaling
+  -algorithm:svm:scaling
+  #if " " in str($param_algorithm_svm_scaling):
+    "$param_algorithm_svm_scaling"
+  #else
+    $param_algorithm_svm_scaling
+  #end if
 #end if
 #if $param_algorithm_svm_scaling_lower:
   -algorithm:svm:scaling_lower $param_algorithm_svm_scaling_lower
@@ -106,7 +121,12 @@
   -algorithm:svm:svc:nu $param_algorithm_svm_svc_nu
 #end if
 #if $param_algorithm_svm_svc_balancing:
-  -algorithm:svm:svc:balancing $param_algorithm_svm_svc_balancing
+  -algorithm:svm:svc:balancing
+  #if " " in str($param_algorithm_svm_svc_balancing):
+    "$param_algorithm_svm_svc_balancing"
+  #else
+    $param_algorithm_svm_svc_balancing
+  #end if
 #end if
 #if $param_algorithm_svm_svc_degree_start:
   -algorithm:svm:svc:degree_start $param_algorithm_svm_svc_degree_start
diff -r 2b1637506673 -r 773e6b46489a readme.md
--- a/readme.md	Wed Mar 01 10:06:57 2017 -0500
+++ b/readme.md	Tue Apr 18 15:55:47 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.: