# HG changeset patch
# User galaxyp
# Date 1492544225 14400
# Node ID 3c7bc75f11bd36e402040f2e47726cf0538ec4b9
# Parent  8f48a6c74368f4663ef59341f341c52ae1672380
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 8f48a6c74368 -r 3c7bc75f11bd IDPosteriorErrorProbability.xml
--- a/IDPosteriorErrorProbability.xml	Wed Mar 01 10:12:24 2017 -0500
+++ b/IDPosteriorErrorProbability.xml	Tue Apr 18 15:37:05 2017 -0400
@@ -44,7 +44,12 @@
   -fit_algorithm:number_of_bins $adv_opts.param_fit_algorithm_number_of_bins
 #end if
     #if $adv_opts.param_fit_algorithm_incorrectly_assigned:
-  -fit_algorithm:incorrectly_assigned $adv_opts.param_fit_algorithm_incorrectly_assigned
+  -fit_algorithm:incorrectly_assigned
+  #if " " in str($adv_opts.param_fit_algorithm_incorrectly_assigned):
+    "$adv_opts.param_fit_algorithm_incorrectly_assigned"
+  #else
+    $adv_opts.param_fit_algorithm_incorrectly_assigned
+  #end if
 #end if
     #if $adv_opts.param_fit_algorithm_max_nr_iterations:
   -fit_algorithm:max_nr_iterations $adv_opts.param_fit_algorithm_max_nr_iterations
diff -r 8f48a6c74368 -r 3c7bc75f11bd readme.md
--- a/readme.md	Wed Mar 01 10:12:24 2017 -0500
+++ b/readme.md	Tue Apr 18 15:37:05 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.: