Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 67:43252277cb23 draft

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author greg
date Tue, 28 Feb 2017 11:08:00 -0500
parents 6d93b214ec55
children 34dcfb570551
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66:6d93b214ec55 67:43252277cb23
14 <command> 14 <command>
15 <![CDATA[ 15 <![CDATA[
16 #import os 16 #import os
17 #import sys 17 #import sys
18 18
19 #set input_format = $input_format_cond.input_format
20 #if str($input_format) == 'ptorthocs':
21 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond
22 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
23 #if str($multiple_codon_alignments) == 'yes':
24 --sequence_type $multiple_codon_alignments_cond.sequence_type
25 #end if
26 #end if
27
28 #if str($options_type.options_type_selector) == 'advanced': 19 #if str($options_type.options_type_selector) == 'advanced':
29 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond 20 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond
30 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments 21 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
31 #if str($multiple_sequence_alignments) == 'yes': 22 #if str($multiple_sequence_alignments) == 'yes':
32 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond 23 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
33 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option 24 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
34 #set generate_output_aln = True 25 #set generate_output_aln = True
35 #else: 26 #else:
36 #set generate_output_aln = False 27 #set generate_output_aln = False
37 #end if 28 #end if
29 #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
30 #set generate_output_tree = True
31 #else:
32 #set generate_output_tree = False
33 #end if
38 #else: 34 #else:
39 #set generate_output_aln = False 35 #set generate_output_aln = False
40 #end if
41
42 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
43 #set generate_output_tree = True
44 #else:
45 #set generate_output_tree = False 36 #set generate_output_tree = False
46 #end if 37 #end if
47 38
48 python $__tool_directory__/phylogenomics_analysis.py 39 python $__tool_directory__/phylogenomics_analysis.py
49 --num_threads \${GALAXY_SLOTS:-4} 40 --num_threads \${GALAXY_SLOTS:-4}
41 #set input_format = $input_format_cond.input_format
50 #if str($input_format) == 'ptortho': 42 #if str($input_format) == 'ptortho':
51 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 43 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
52 #else: 44 #else:
53 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 45 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
54 --orthogroup_fna 'true' 46 --orthogroup_fna 'true'
47 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond
48 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
49 #if str($multiple_codon_alignments) == 'yes':
50 --sequence_type $multiple_codon_alignments_cond.sequence_type
51 #end if
55 #end if 52 #end if
56 --config_dir '$scaffold.fields.path' 53 --config_dir '$scaffold.fields.path'
57 --scaffold '$scaffold.fields.path' 54 --scaffold '$scaffold.fields.path'
58 --method $method 55 --method $method
59 56