# HG changeset patch
# User galaxyp
# Date 1492545709 14400
# Node ID bf3b4e5c0dcbad2b00e535557b40867b0d691e33
# Parent  53f456ded5a63402496039e0b855761f94f91702
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb

diff -r 53f456ded5a6 -r bf3b4e5c0dcb DecoyDatabase.xml
--- a/DecoyDatabase.xml	Wed Mar 01 12:16:29 2017 -0500
+++ b/DecoyDatabase.xml	Tue Apr 18 16:01:49 2017 -0400
@@ -23,13 +23,28 @@
   -decoy_string     "$param_decoy_string"
 #end if
 #if $param_decoy_string_position:
-  -decoy_string_position $param_decoy_string_position
+  -decoy_string_position
+  #if " " in str($param_decoy_string_position):
+    "$param_decoy_string_position"
+  #else
+    $param_decoy_string_position
+  #end if
 #end if
 #if $param_append:
-  -append $param_append
+  -append
+  #if " " in str($param_append):
+    "$param_append"
+  #else
+    $param_append
+  #end if
 #end if
 #if $param_method:
-  -method $param_method
+  -method
+  #if " " in str($param_method):
+    "$param_method"
+  #else
+    $param_method
+  #end if
 #end if
 #if $adv_opts.adv_opts_selector=='advanced':
     #if $adv_opts.param_force:
@@ -73,14 +88,12 @@
   <outputs>
     <data name="param_out" format="fasta"/>
   </outputs>
-
-   <tests>
-        <test>
-            <param name="param_in" value="DecoyDatabase_input.fasta"/>
-            <output name="param_out" file="DecoyDatabase_output.fasta"/>
-        </test>
-    </tests>
-
+  <tests>
+    <test>
+        <param name="param_in" value="DecoyDatabase_input.fasta"/>
+        <output name="param_out" file="DecoyDatabase_output.fasta"/>
+    </test>
+  </tests>
   <help>Create decoy peptide databases from normal ones.
 
 
diff -r 53f456ded5a6 -r bf3b4e5c0dcb readme.md
--- a/readme.md	Wed Mar 01 12:16:29 2017 -0500
+++ b/readme.md	Tue Apr 18 16:01:49 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.: