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comparison phylogenomics_analysis.xml @ 28:a401feff8354 draft

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author greg
date Tue, 10 Jan 2017 12:26:30 -0500
parents ce6108b3063b
children 7d0cc822c94e
comparison
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27:ce6108b3063b 28:a401feff8354
69 #else if str($multiple_sequence_alignments_option) == 'add_alignments': 69 #else if str($multiple_sequence_alignments_option) == 'add_alignments':
70 #set multiple_sequence_alignments_option_str = 'Add proteins to alignments (MAFFT algorithm)' 70 #set multiple_sequence_alignments_option_str = 'Add proteins to alignments (MAFFT algorithm)'
71 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments': 71 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
72 #set multiple_sequence_alignments_option_str = 'Create alignments (PASTA algorithm)' 72 #set multiple_sequence_alignments_option_str = 'Create alignments (PASTA algorithm)'
73 #end if 73 #end if
74
74 #set input_includes_coding_sequences_cond = $options_type.multiple_sequence_alignments_cond.input_includes_coding_sequences_cond 75 #set input_includes_coding_sequences_cond = $options_type.multiple_sequence_alignments_cond.input_includes_coding_sequences_cond
75 #set input_includes_coding_sequences = $input_includes_coding_sequences_cond.input_includes_coding_sequences 76 #set input_includes_coding_sequences = $input_includes_coding_sequences_cond.input_includes_coding_sequences
76 #if str($input_includes_coding_sequences) == 'yes': 77 #if str($input_includes_coding_sequences) == 'yes':
77 #set multiple_codon_alignments_cond = $input_includes_coding_sequences_cond.multiple_codon_alignments_cond 78 #set multiple_codon_alignments_cond = $input_includes_coding_sequences_cond.multiple_codon_alignments_cond
78 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments 79 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
79 #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond 80 #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
80 #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences 81 #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences
81 #end if 82 #end if
83
82 #if str($multiple_sequence_alignments_option) == 'create_alignments': 84 #if str($multiple_sequence_alignments_option) == 'create_alignments':
83 --create_alignments 85 --create_alignments
84 #else if str($multiple_sequence_alignments_option) == 'add_alignments': 86 #else if str($multiple_sequence_alignments_option) == 'add_alignments':
85 --add_alignments 87 --add_alignments
86 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments': 88 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
87 --pasta_alignments 89 --pasta_alignments
88 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit 90 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
89 #end if 91 #end if
92
90 #if str($input_includes_coding_sequences) == 'yes': 93 #if str($input_includes_coding_sequences) == 'yes':
91 #if str($multiple_codon_alignments) == 'yes': 94 #if str($multiple_codon_alignments) == 'yes':
92 --codon_alignments 95 --codon_alignments
93 #if str($use_corresponding_coding_sequences) == 'yes': 96 #if str($use_corresponding_coding_sequences) == 'yes':
94 #if $num_orthogroup_fna == 0: 97 #if $num_orthogroup_fna == 0:
281 </when> 284 </when>
282 </conditional> 285 </conditional>
283 </inputs> 286 </inputs>
284 <outputs> 287 <outputs>
285 <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/> 288 <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/>
286 <data name="output_aln" format="txt" label="Multiple sequence alignments using method '${multiple_sequence_alignments_option_str}' on ${on_string}"> 289 <data name="output_aln" format="txt" label="${multiple_sequence_alignments_option_str} on ${on_string}">
287 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter> 290 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
288 </data> 291 </data>
289 <data name="output_tree" format="txt" label="Phylogenetic trees on ${on_string}"> 292 <data name="output_tree" format="txt" label="Phylogenetic trees on ${on_string}">
290 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter> 293 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
291 </data> 294 </data>