Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 39:0e7ad3fa851e draft

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author greg
date Tue, 01 Aug 2017 11:43:49 -0400
parents bfac5c2309ca
children 72f519a8e79a
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38:bfac5c2309ca 39:0e7ad3fa851e
129 </data> 129 </data>
130 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}"> 130 <data name="output_aln_trimmed_ca" format="ptaligntrimmedca" label="${tool.name} (trimmed protein and coding sequences orthogroup alignments) on ${on_string}">
131 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter> 131 <filter>(input_format_cond['input_format'] == 'ptortho' or (input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes')) and (remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no')</filter>
132 </data> 132 </data>
133 <collection name="dataset_collection" type="list" label="${tool.name} (dataset collection) on ${on_string}"> 133 <collection name="dataset_collection" type="list" label="${tool.name} (dataset collection) on ${on_string}">
134 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/dataset_collection" format="fasta" /> 134 <discover_datasets pattern="__name__" directory="dataset_collection" format="fasta" />
135 <filter>output_dataset_collection_cond['output_dataset_collection'] == 'yes'</filter> 135 <filter>output_dataset_collection_cond['output_dataset_collection'] == 'yes'</filter>
136 </collection> 136 </collection>
137 </outputs> 137 </outputs>
138 <tests> 138 <tests>
139 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed. 139 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.