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comparison phylogenomics_analysis.xml @ 22:bacaa8a6e45d draft

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author greg
date Sat, 07 Jan 2017 09:58:17 -0500
parents 86a469a50fc4
children 48479c94a6f3
comparison
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21:86a469a50fc4 22:bacaa8a6e45d
31 #set num_orthogroup_fna = $len([f for f in $os.listdir($input_extra_files_path) if f.endswith('.fna')]) 31 #set num_orthogroup_fna = $len([f for f in $os.listdir($input_extra_files_path) if f.endswith('.fna')])
32 32
33 #set src_fasta_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta') 33 #set src_fasta_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
34 #set dest_fasta_dir = $output_fasta.extra_files_path 34 #set dest_fasta_dir = $output_fasta.extra_files_path
35 35
36 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option) == 'pasta_alignments': 36 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments) == 'yes':
37 #set generate_output_aln = True 37 #set generate_output_aln = True
38 #set src_aln_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_aln') 38 #set src_aln_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_aln')
39 #set dest_aln_dir = $output_aln.extra_files_path 39 #set dest_aln_dir = $output_aln.extra_files_path
40 mkdir -p $dest_aln_dir && 40 mkdir -p $dest_aln_dir &&
41 #else: 41 #else:
275 </conditional> 275 </conditional>
276 </inputs> 276 </inputs>
277 <outputs> 277 <outputs>
278 <data name="output_fasta" format="txt" label="Sequence alignments and corresponding phylogenies on ${on_string}"/> 278 <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}"> 279 <data name="output_aln" format="txt" label="Sequence alignments and corresponding phylogenies using PASTA on ${on_string}">
280 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option'] == 'pasta_alignments'</filter> 280 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
281 </data> 281 </data>
282 <data name="output_tree" format="txt" label="Phylogenetic trees on ${on_string}"> 282 <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> 283 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
284 </data> 284 </data>
285 </outputs> 285 </outputs>