Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 47:ee70ebb1ca4e draft

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Uploaded
author greg
date Fri, 08 Sep 2017 08:33:26 -0400
parents cebcf6f7cff2
children 4e660a64437c
comparison
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46:31f85a5aefc0 47:ee70ebb1ca4e
67 </when> 67 </when>
68 </conditional> 68 </conditional>
69 <expand macro="cond_remove_gappy_sequences" /> 69 <expand macro="cond_remove_gappy_sequences" />
70 </inputs> 70 </inputs>
71 <outputs> 71 <outputs>
72 <collection name="primary" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}"> 72 <collection name="primary_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
73 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln" format="fasta" /> 73 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_faa" format="fasta" />
74 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 74 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
75 </collection> 75 </collection>
76 <collection name="trimmed" type="list" label="${tool.name} (trimmed proteins orthogroup alignments) on ${on_string}"> 76 <collection name="primary_fna" type="list" label="${tool.name} (primary orthogroup codon alignments) on ${on_string}">
77 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln" format="fasta" /> 77 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_fna" format="fasta" />
78 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
79 </collection>
80 <collection name="trimmed_faa" type="list" label="${tool.name} (trimmed orthogroup protein alignments) on ${on_string}">
81 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_faa" format="fasta" />
78 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter> 82 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
79 </collection> 83 </collection>
80 <collection name="primary_trimmed" type="list" label="${tool.name} (primary proteins orthogroup alignments) on ${on_string}"> 84 <collection name="primary_trimmed" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
81 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" /> 85 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
82 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter> 86 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
83 </collection> 87 </collection>
84 <collection name="filtered" type="list" label="${tool.name} (filtered proteins orthogroup alignments) on ${on_string}"> 88 <collection name="trimmed_fna" type="list" label="${tool.name} (trimmed orthogroup codon alignments) on ${on_string}">
85 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln" format="fasta" /> 89 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_fna" format="fasta" />
90 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
91 </collection>
92 <collection name="primary_trimmed" type="list" label="${tool.name} (primary orthogroup protein and codon alignments) on ${on_string}">
93 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
94 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
95 </collection>
96 <collection name="filtered" type="list" label="${tool.name} (filtered orthogroup protein alignments) on ${on_string}">
97 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_faa" format="fasta" />
86 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> 98 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
87 </collection> 99 </collection>
88 <collection name="primary_filtered" type="list" label="${tool.name} (primary and trimmed proteins orthogroup alignments) on ${on_string}"> 100 <collection name="primary_filtered" type="list" label="${tool.name} (primary and trimmed proteins orthogroup alignments) on ${on_string}">
89 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" /> 101 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
90 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> 102 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter>
103 </collection>
104 <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
105 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
106 <filter>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'] == 'yes'</filter>
91 </collection> 107 </collection>
92 </outputs> 108 </outputs>
93 <tests> 109 <tests>
94 <test> 110 <test>
95 </test> 111 </test>