changeset 1:79017f4e6ead draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author galaxyp
date Tue, 18 Apr 2017 15:58:11 -0400
parents 9c63c85a3cf5
children 6bfb4c92d4fd
files AccurateMassSearch.xml readme.md
diffstat 2 files changed, 14 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/AccurateMassSearch.xml	Wed Mar 01 12:24:55 2017 -0500
+++ b/AccurateMassSearch.xml	Tue Apr 18 15:58:11 2017 -0400
@@ -39,10 +39,20 @@
   -algorithm:mass_error_value $param_algorithm_mass_error_value
 #end if
 #if $param_algorithm_mass_error_unit:
-  -algorithm:mass_error_unit $param_algorithm_mass_error_unit
+  -algorithm:mass_error_unit
+  #if " " in str($param_algorithm_mass_error_unit):
+    "$param_algorithm_mass_error_unit"
+  #else
+    $param_algorithm_mass_error_unit
+  #end if
 #end if
 #if $param_algorithm_ionization_mode:
-  -algorithm:ionization_mode $param_algorithm_ionization_mode
+  -algorithm:ionization_mode
+  #if " " in str($param_algorithm_ionization_mode):
+    "$param_algorithm_ionization_mode"
+  #else
+    $param_algorithm_ionization_mode
+  #end if
 #end if
 #if $param_algorithm_isotopic_similarity:
   -algorithm:isotopic_similarity
--- a/readme.md	Wed Mar 01 12:24:55 2017 -0500
+++ b/readme.md	Tue Apr 18 15:58:11 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.: