Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 50:85b11211fe87 draft

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Uploaded
author greg
date Fri, 08 Sep 2017 09:22:23 -0400
parents 4e660a64437c
children ad8032da13b9
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49:4e660a64437c 50:85b11211fe87
77 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_faa" format="fasta" /> 77 <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> 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>
79 </collection> 79 </collection>
80 <collection name="pristine_trimmed_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}"> 80 <collection name="pristine_trimmed_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
81 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" /> 81 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
82 <filter>input_format_cond['input_format'] == 'ptortho' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter> 82 <filter>input_format_cond['input_format'] == 'ptortho' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
83 </collection> 83 </collection>
84 <collection name="filtered_faa" type="list" label="${tool.name} (filtered orthogroup protein alignments) on ${on_string}"> 84 <collection name="filtered_faa" type="list" label="${tool.name} (filtered orthogroup protein alignments) on ${on_string}">
85 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_faa" format="fasta" /> 85 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_faa" format="fasta" />
86 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> 86 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
87 </collection> 87 </collection>
88 <collection name="pristine_filtered_faa" type="list" label="${tool.name} (primary and trimmed proteins orthogroup alignments) on ${on_string}"> 88 <collection name="pristine_filtered_faa" type="list" label="${tool.name} (primary and trimmed proteins orthogroup alignments) on ${on_string}">
89 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" /> 89 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
90 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter> 90 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
91 </collection> 91 </collection>
92 <collection name="primary_fna" type="list" label="${tool.name} (primary orthogroup codon alignments) on ${on_string}"> 92 <collection name="primary_fna" type="list" label="${tool.name} (primary orthogroup codon alignments) on ${on_string}">
93 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_fna" format="fasta" /> 93 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_fna" format="fasta" />
94 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 94 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>
95 </collection> 95 </collection>
97 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_fna" format="fasta" /> 97 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_trimmed_aln_fna" format="fasta" />
98 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter> 98 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
99 </collection> 99 </collection>
100 <collection name="pristine_trimmed_fna" type="list" label="${tool.name} (primary orthogroup protein and codon alignments) on ${on_string}"> 100 <collection name="pristine_trimmed_fna" type="list" label="${tool.name} (primary orthogroup protein and codon alignments) on ${on_string}">
101 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" /> 101 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
102 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter> 102 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'no'</filter>
103 </collection> 103 </collection>
104 <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}"> 104 <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
105 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" /> 105 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
106 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter> 106 <filter>input_format_cond['input_format'] == 'ptorthocs' and input_format_cond['codon_alignments'] == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
107 </collection> 107 </collection>
108 <collection name="pristine_filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}"> 108 <collection name="pristine_filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
109 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" /> 109 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/other_orthogroups_aln" format="fasta" />
110 <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' and remove_gappy_sequences_cond['output_pristine_alignments'] == 'yes'</filter> 110 <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>
111 </collection> 111 </collection>
112 </outputs> 112 </outputs>
113 <tests> 113 <tests>
114 <test> 114 <test>
115 </test> 115 </test>