# HG changeset patch
# User galaxyp
# Date 1492543894 14400
# Node ID ded742713fecee84554b3c894d1e44fbab4b7a3c
# Parent  6cf7e57d3e6ed7ab401abaa604d4ba7aaf99358d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 6cf7e57d3e6e -r ded742713fec FeatureFinderCentroided.xml
--- a/FeatureFinderCentroided.xml	Wed Mar 01 10:03:13 2017 -0500
+++ b/FeatureFinderCentroided.xml	Tue Apr 18 15:31:34 2017 -0400
@@ -55,7 +55,12 @@
   -algorithm:feature:min_score $param_algorithm_feature_min_score
 #end if
 #if $param_algorithm_feature_reported_mz:
-  -algorithm:feature:reported_mz $param_algorithm_feature_reported_mz
+  -algorithm:feature:reported_mz
+  #if " " in str($param_algorithm_feature_reported_mz):
+    "$param_algorithm_feature_reported_mz"
+  #else
+    $param_algorithm_feature_reported_mz
+  #end if
 #end if
 #if $param_algorithm_user_seed_rt_tolerance:
   -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance
@@ -107,7 +112,12 @@
   -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span
 #end if
     #if $adv_opts.param_algorithm_feature_rt_shape:
-  -algorithm:feature:rt_shape $adv_opts.param_algorithm_feature_rt_shape
+  -algorithm:feature:rt_shape
+  #if " " in str($adv_opts.param_algorithm_feature_rt_shape):
+    "$adv_opts.param_algorithm_feature_rt_shape"
+  #else
+    $adv_opts.param_algorithm_feature_rt_shape
+  #end if
 #end if
     #if $adv_opts.param_algorithm_feature_max_intersection:
   -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection
diff -r 6cf7e57d3e6e -r ded742713fec readme.md
--- a/readme.md	Wed Mar 01 10:03:13 2017 -0500
+++ b/readme.md	Tue Apr 18 15:31:34 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.: