# HG changeset patch
# User galaxyp
# Date 1492543691 14400
# Node ID 2ef75ed3d63312722f0fd158883974f5beb9784d
# Parent  2b1f6887cd42f354e858d57fbabfbc108533fbde
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 2b1f6887cd42 -r 2ef75ed3d633 ConsensusID.xml
--- a/ConsensusID.xml	Wed Mar 01 10:09:59 2017 -0500
+++ b/ConsensusID.xml	Tue Apr 18 15:28:11 2017 -0400
@@ -25,7 +25,12 @@
   -mz_delta $param_mz_delta
 #end if
 #if $param_algorithm:
-  -algorithm $param_algorithm
+  -algorithm
+  #if " " in str($param_algorithm):
+    "$param_algorithm"
+  #else
+    $param_algorithm
+  #end if
 #end if
 #if $param_filter_considered_hits:
   -filter:considered_hits $param_filter_considered_hits
@@ -43,7 +48,12 @@
   -PEPIons:min_shared $param_PEPIons_min_shared
 #end if
 #if $param_PEPMatrix_matrix:
-  -PEPMatrix:matrix $param_PEPMatrix_matrix
+  -PEPMatrix:matrix
+  #if " " in str($param_PEPMatrix_matrix):
+    "$param_PEPMatrix_matrix"
+  #else
+    $param_PEPMatrix_matrix
+  #end if
 #end if
 #if $param_PEPMatrix_penalty:
   -PEPMatrix:penalty $param_PEPMatrix_penalty
diff -r 2b1f6887cd42 -r 2ef75ed3d633 readme.md
--- a/readme.md	Wed Mar 01 10:09:59 2017 -0500
+++ b/readme.md	Tue Apr 18 15:28:11 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.: