# HG changeset patch
# User galaxyp
# Date 1492545456 14400
# Node ID 091c5c67ae88fc185699a319f2dd66999c9073e0
# Parent  75e0909240d8bf7576707e05e993de3468c50968
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 75e0909240d8 -r 091c5c67ae88 XTandemAdapter.xml
--- a/XTandemAdapter.xml	Wed Mar 01 10:04:32 2017 -0500
+++ b/XTandemAdapter.xml	Tue Apr 18 15:57:36 2017 -0400
@@ -35,10 +35,20 @@
   -fragment_mass_tolerance $param_fragment_mass_tolerance
 #end if
 #if $param_precursor_error_units:
-  -precursor_error_units $param_precursor_error_units
+  -precursor_error_units
+  #if " " in str($param_precursor_error_units):
+    "$param_precursor_error_units"
+  #else
+    $param_precursor_error_units
+  #end if
 #end if
 #if $param_fragment_error_units:
-  -fragment_error_units $param_fragment_error_units
+  -fragment_error_units
+  #if " " in str($param_fragment_error_units):
+    "$param_fragment_error_units"
+  #else
+    $param_fragment_error_units
+  #end if
 #end if
 #if $param_min_precursor_charge:
   -min_precursor_charge $param_min_precursor_charge
@@ -47,7 +57,12 @@
   -max_precursor_charge $param_max_precursor_charge
 #end if
 #if $param_allow_isotope_error:
-  -allow_isotope_error $param_allow_isotope_error
+  -allow_isotope_error
+  #if " " in str($param_allow_isotope_error):
+    "$param_allow_isotope_error"
+  #else
+    $param_allow_isotope_error
+  #end if
 #end if
 
 #if $rep_param_fixed_modifications:
@@ -78,10 +93,20 @@
   -minimum_fragment_mz $param_minimum_fragment_mz
 #end if
 #if $param_cleavage_site:
-  -cleavage_site $param_cleavage_site
+  -cleavage_site
+  #if " " in str($param_cleavage_site):
+    "$param_cleavage_site"
+  #else
+    $param_cleavage_site
+  #end if
 #end if
 #if $param_output_results:
-  -output_results $param_output_results
+  -output_results
+  #if " " in str($param_output_results):
+    "$param_output_results"
+  #else
+    $param_output_results
+  #end if
 #end if
 #if $param_max_valid_expect:
   -max_valid_expect $param_max_valid_expect
diff -r 75e0909240d8 -r 091c5c67ae88 readme.md
--- a/readme.md	Wed Mar 01 10:04:32 2017 -0500
+++ b/readme.md	Tue Apr 18 15:57:36 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.: