Mercurial > repos > sanbi-uwc > novo_align
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(-) [+] |
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--- 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>