changeset 33:fc134b9ac951 draft

planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit a5e4ca4a66eb4e315ca564238e27e03936eea6fa
author sanbi-uwc
date Thu, 31 May 2018 04:46:32 -0400
parents c6e99afd59a8
children 093b3752ca89
files novo_align.py novo_align.xml
diffstat 2 files changed, 4 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/novo_align.py	Thu May 31 03:45:15 2018 -0400
+++ b/novo_align.py	Thu May 31 04:46:32 2018 -0400
@@ -34,7 +34,7 @@
 def main():
     parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
     parser.add_argument('out_file')
-    parser.add_argument('out_stats')    
+    parser.add_argument('--out_stats')    
     parser.add_argument('--index_filename')
     parser.add_argument('--forward_filename')
     parser.add_argument('--reverse_filename')
--- a/novo_align.xml	Thu May 31 03:45:15 2018 -0400
+++ b/novo_align.xml	Thu May 31 04:46:32 2018 -0400
@@ -43,6 +43,7 @@
         #end if
         python $__tool_directory__/novo_align.py
             '${out_file}'
+            '${out_stats}'
             --index
             #if str($index.source) == 'builtin':
               '${index.index1.fields.path}'
@@ -123,7 +124,8 @@
         </param>
     </inputs>-->
     <outputs>
-        <data format="bam" name="out_file" />
+        <data format="sam" name="out_file" />
+        <data format="text" name="out_stats" />
     </outputs>
     <tests>
         <test>