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comparison phylogenomics_analysis.xml @ 44:3592048fb258 draft

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author greg
date Fri, 03 Feb 2017 13:46:21 -0500
parents 923a54b9425c
children c27c13bb4615
comparison
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43:923a54b9425c 44:3592048fb258
21 #set scaffold_path = $scaffold.fields.path 21 #set scaffold_path = $scaffold.fields.path
22 #set scaffold_dir = $os.path.split($scaffold_path)[0] 22 #set scaffold_dir = $os.path.split($scaffold_path)[0]
23 #set scaffold_selection = $os.path.split($scaffold_path)[1] 23 #set scaffold_selection = $os.path.split($scaffold_path)[1]
24 #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln') 24 #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln')
25 #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta') 25 #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta')
26 #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree' 26 #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree')
27 27
28 #if str($input_format) == 'ptcgf': 28 #if str($input_format) == 'ptcgf':
29 #set dest_fasta_dir = $output_fasta_ptcgf.extra_files_path 29 #set dest_fasta_dir = $output_fasta_ptcgf.extra_files_path
30 #set multiple_codon_alignments = 'no' 30 #set multiple_codon_alignments = 'no'
31 #set use_corresponding_coding_sequences = 'no 31 #set use_corresponding_coding_sequences = 'no
32 #else: 32 #else:
33 ## str($input_format) == 'ptcgfcs':
34 #set dest_fasta_dir = $output_fasta_ptcgfcs.extra_files_path 33 #set dest_fasta_dir = $output_fasta_ptcgfcs.extra_files_path
35 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond 34 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond
36 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments 35 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
37 #if str($multiple_codon_alignments) == 'yes': 36 #if str($multiple_codon_alignments) == 'yes':
38 #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond 37 #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
63 #else: 62 #else:
64 #set generate_output_tree = False 63 #set generate_output_tree = False
65 #end if 64 #end if
66 65
67 PhylogenomicsAnalysis 66 PhylogenomicsAnalysis
68 --num_threads '\${GALAXY_SLOTS:-4}' 67 --num_threads \${GALAXY_SLOTS:-4}
69 --orthogroup_faa '$input.extra_files_path' 68 --orthogroup_faa '$input.extra_files_path'
70 --scaffold_dir '$scaffold_dir' 69 --scaffold_dir '$scaffold_dir'
71 --scaffold '$scaffold_selection' 70 --scaffold '$scaffold_selection'
72 --method $method 71 --method $method
73 72