Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 58:1b256588fb06 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Mon, 13 Feb 2017 09:33:37 -0500
parents c662ff5166df
children 963f84101cdc
comparison
equal deleted inserted replaced
57:c662ff5166df 58:1b256588fb06
17 #import os 17 #import os
18 #import sys 18 #import sys
19 19
20 #set input_format = $input_format_cond.input_format 20 #set input_format = $input_format_cond.input_format
21 #set pipeline_output_dir = 'phylogenomicsAnalysis_dir' 21 #set pipeline_output_dir = 'phylogenomicsAnalysis_dir'
22 #set scaffold_path = $scaffold.fields.path
23 #set scaffold_dir = $os.path.split($scaffold_path)[0]
24 #set scaffold_selection = $os.path.split($scaffold_path)[1]
25 #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln') 22 #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln')
26 #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta') 23 #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta')
27 #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree') 24 #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree')
28 25
29 #if str($input_format) == 'ptortho': 26 #if str($input_format) == 'ptortho':
73 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 70 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
74 #else: 71 #else:
75 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 72 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
76 --orthogroup_fna 73 --orthogroup_fna
77 #end if 74 #end if
78 --scaffold_dir '$scaffold_dir' 75 --scaffold '$scaffold.fields.path'
79 --scaffold '$scaffold_selection'
80 --method $method 76 --method $method
81 77
82 #if str($options_type.options_type_selector) == 'advanced': 78 #if str($options_type.options_type_selector) == 'advanced':
83 #if str($multiple_sequence_alignments) == 'yes': 79 #if str($multiple_sequence_alignments) == 'yes':
84 #if str($multiple_sequence_alignments_option) == 'create_alignments': 80 #if str($multiple_sequence_alignments_option) == 'create_alignments':