Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 19:953e13d2940b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Sat, 07 Jan 2017 09:43:27 -0500
parents 7d622f6a4732
children d34a42c6affb
comparison
equal deleted inserted replaced
18:7d622f6a4732 19:953e13d2940b
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' and str($options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option == 'pasta_alignments':
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: