Mercurial > repos > greg > gene_family_aligner
changeset 8:9e68bebb3d7c draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 10 Apr 2017 10:55:45 -0400 |
| parents | 529f4635ddb4 |
| children | 43341e97bb08 |
| files | gene_family_aligner.xml |
| diffstat | 1 files changed, 20 insertions(+), 3 deletions(-) [+] |
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--- a/gene_family_aligner.xml Mon Apr 10 09:37:45 2017 -0400 +++ b/gene_family_aligner.xml Mon Apr 10 10:55:45 2017 -0400 @@ -47,11 +47,20 @@ #if str($remove_sequences_with_gaps) == 'yes': --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment + --output '$output_aln_filtered' + --output_dir '$output_aln_filtered.files_path' + #else: + --output '$output_aln_trimmed' + --output_dir '$output_aln_trimmed.files_path' #end if + #else: + --output '$output_aln' + --output_dir '$output_aln.files_path' #end if + #esle: + --output '$output_aln' + --output_dir '$output_aln.files_path' #end if - --output '$output' - --output_dir '$output.files_path' ]]> </command> <inputs> @@ -83,7 +92,15 @@ </conditional> </inputs> <outputs> - <data name="output" format="ptalign" label="Aligned gene family sequences on ${on_string}" /> + <data name="output_aln" format="ptalign" label="Aligned gene family sequences on ${on_string}"> + <filter>options_type_cond['options_type'] == 'basic' or (options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'no')</filter> + </data> + <data name="output_aln_filtered" format="ptalignfiltered" label="Filtered aligned gene family sequences on ${on_string}"> + <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> + </data> + <data name="output_aln_trimmed" format="ptaligntrimmed" label="Trimmed aligned gene family sequences on ${on_string}"> + <filter>options_type_cond['options_type'] == 'advanced' and options_type_cond['remove_gappy_sequences_cond']['remove_gappy_sequences'] == 'yes' and options_type_cond['remove_gappy_sequences_cond']['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter> + </data> </outputs> <tests> <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.