Mercurial > repos > galaxyp > openms_xtandemadapter

changeset 5:c8b225c69a7f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 8a95bc868914fb41c7452907f73a9273b03286ab
author galaxyp
date Thu, 11 Jan 2018 17:52:13 -0500
parents 7b5457bd6112
children b09039836cb1
files XTandemAdapter.xml readme.md
diffstat 2 files changed, 11 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/XTandemAdapter.xml	Thu Nov 09 06:12:04 2017 -0500
+++ b/XTandemAdapter.xml	Thu Jan 11 17:52:13 2018 -0500
@@ -92,7 +92,7 @@
     $param_enzyme
   #end if
 #end if
-#if $param_missed_cleavages:
+#if str($param_missed_cleavages) != '':
   -missed_cleavages $param_missed_cleavages
 #end if
 #if $param_semi_cleavage:
--- a/readme.md	Thu Nov 09 06:12:04 2017 -0500
+++ b/readme.md	Thu Jan 11 17:52:13 2018 -0500
@@ -117,7 +117,14 @@
     [...]
     ]]>
     ```
-    
+ 
+ * In Xtandem Converter and probably in others:
+ 
+    ```
+    #if str($param_missed_cleavages) != '':
+    ```
+    This is because integers needs to be compared as string otherwise `0` becomes `false`.
+ 
  * In `MetaProSIP.xml` add `R` as a requirement:
  
    ```
@@ -164,7 +171,8 @@
     ```
     
 
- * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in Galaxy-stable and are therefore in `SKIP_TOOLS_FILES.txt`:
+ * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in
+   by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`:
     * SeedListGenerator
     * SpecLibSearcher
     * MapAlignerIdentification