Mercurial > repos > greg > gene_family_aligner
changeset 2:01c08c35d051 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 07 Apr 2017 13:19:26 -0400 |
| parents | 4f1c3b8c9ab1 |
| children | 962feb5f0818 |
| files | gene_family_aligner.py gene_family_aligner.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/gene_family_aligner.py Fri Apr 07 13:13:38 2017 -0400 +++ b/gene_family_aligner.py Fri Apr 07 13:19:26 2017 -0400 @@ -36,8 +36,8 @@ if args.pasta_iter_limit is not None: cmd += ' --pasta_iter_limit %d' % args.pasta_iter_limit cmd += ' --num_threads %d' % args.num_threads -if args.orthogroup_fna is not None: - cmd += ' --orthogroup_fna' +if args.codon_alignments is not None: + cmd += ' --codon_alignments' if args.automated_trimming is not None: cmd += ' --automated_trimming' if args.gap_trimming is not None:
--- a/gene_family_aligner.xml Fri Apr 07 13:13:38 2017 -0400 +++ b/gene_family_aligner.xml Fri Apr 07 13:19:26 2017 -0400 @@ -89,10 +89,10 @@ </inputs> <outputs> <data name="output_ptortho" format="ptortho" label="Integrated gene family clusters on ${on_string}"> - <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'no')</filter> + <filter>input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'no')</filter> </data> <data name="output_ptorthocs" format="ptorthocs" label="Integrated gene family clusters and corresponding coding sequences on ${on_string}"> - <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['orthogroup_fna'] == 'yes'</filter> + <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes'</filter> </data> </outputs> <tests>