Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 27:ce6108b3063b draft

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author greg
date Tue, 10 Jan 2017 12:21:47 -0500
parents e19872abae29
children a401feff8354
comparison
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26:e19872abae29 27:ce6108b3063b
62 62
63 #if str($options_type.options_type_selector) == 'advanced': 63 #if str($options_type.options_type_selector) == 'advanced':
64 #if str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes': 64 #if str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes':
65 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond 65 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
66 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option 66 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
67 #if str($multiple_sequence_alignments_option) == 'create_alignments':
68 #set multiple_sequence_alignments_option_str = 'Create alignments (MAFFT algorithm)'
69 #else if str($multiple_sequence_alignments_option) == 'add_alignments':
70 #set multiple_sequence_alignments_option_str = 'Add proteins to alignments (MAFFT algorithm)'
71 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
72 #set multiple_sequence_alignments_option_str = 'Create alignments (PASTA algorithm)'
73 #end if
67 #set input_includes_coding_sequences_cond = $options_type.multiple_sequence_alignments_cond.input_includes_coding_sequences_cond 74 #set input_includes_coding_sequences_cond = $options_type.multiple_sequence_alignments_cond.input_includes_coding_sequences_cond
68 #set input_includes_coding_sequences = $input_includes_coding_sequences_cond.input_includes_coding_sequences 75 #set input_includes_coding_sequences = $input_includes_coding_sequences_cond.input_includes_coding_sequences
69 #if str($input_includes_coding_sequences) == 'yes': 76 #if str($input_includes_coding_sequences) == 'yes':
70 #set multiple_codon_alignments_cond = $input_includes_coding_sequences_cond.multiple_codon_alignments_cond 77 #set multiple_codon_alignments_cond = $input_includes_coding_sequences_cond.multiple_codon_alignments_cond
71 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments 78 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
274 </when> 281 </when>
275 </conditional> 282 </conditional>
276 </inputs> 283 </inputs>
277 <outputs> 284 <outputs>
278 <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/> 285 <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/>
279 <data name="output_aln" format="txt" label="Sequence alignments and corresponding phylogenies using PASTA on ${on_string}"> 286 <data name="output_aln" format="txt" label="Multiple sequence alignments using method '${multiple_sequence_alignments_option_str}' on ${on_string}">
280 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter> 287 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
281 </data> 288 </data>
282 <data name="output_tree" format="txt" label="Phylogenetic trees on ${on_string}"> 289 <data name="output_tree" format="txt" label="Phylogenetic trees on ${on_string}">
283 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter> 290 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
284 </data> 291 </data>