Mercurial > repos > greg > gene_family_aligner

comparison gene_family_aligner.xml @ 36:264c72346d0f draft

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author greg
date Thu, 08 Jun 2017 09:45:07 -0400
parents e58f6138188c
children bfac5c2309ca
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35:e58f6138188c 36:264c72346d0f
2 <description>aligns integrated orthologous gene family clusters</description> 2 <description>aligns integrated orthologous gene family clusters</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_gene_family_aligner" /> 6 <expand macro="requirements_gene_family_aligner" />
7 <command detect_errors="exit_code"> 7 <command detect_errors="exit_code"><![CDATA[
8 <![CDATA[ 8 #set input_format = $input_format_cond.input_format
9 #set input_format = $input_format_cond.input_format 9 #set alignment_method_cond = $input_format_cond.alignment_method_cond
10 #set alignment_method_cond = $input_format_cond.alignment_method_cond 10 #set alignment_method = $alignment_method_cond.alignment_method
11 #set alignment_method = $alignment_method_cond.alignment_method 11 #if str($input_format_cond.input_format) == 'ptortho':
12 #if str($input_format_cond.input_format) == 'ptortho': 12 #set output_codon_alignments = False
13 #set output_codon_alignments = False 13 #else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no':
14 #else if str($input_format_cond.input_format) == 'ptorthocs' and str($input_format_cond.codon_alignments ) == 'no': 14 #set output_codon_alignments = False
15 #set output_codon_alignments = False 15 #else:
16 #else: 16 #set output_codon_alignments = True
17 #set output_codon_alignments = True 17 #end if
18 #end if 18
19 19 python $__tool_directory__/gene_family_aligner.py
20 python $__tool_directory__/gene_family_aligner.py 20 --alignment_method $alignment_method
21 --alignment_method $alignment_method 21 #if str($alignment_method) == 'pasta':
22 #if str($alignment_method) == 'pasta': 22 --pasta_script_path '$__tool_directory__/run_pasta.py'
23 --pasta_script_path '$__tool_directory__/run_pasta.py' 23 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit
24 --pasta_iter_limit $alignment_method_cond.pasta_iter_limit 24 #end if
25 #end if 25 --num_threads \${GALAXY_SLOTS:-4}
26 --num_threads \${GALAXY_SLOTS:-4} 26 #if str($input_format) == 'ptortho':
27 #if str($input_format) == 'ptortho': 27 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
28 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 28 #else:
29 #else: 29 ## str($input_format) == 'ptorthocs'
30 ## str($input_format) == 'ptorthocs' 30 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
31 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 31 #if str($input_format_cond.codon_alignments) == 'yes':
32 #if str($input_format_cond.codon_alignments) == 'yes': 32 --codon_alignments 'true'
33 --codon_alignments 'true' 33 #end if
34 #end if 34 #end if
35 #end if 35 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
36 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 36 #if str($remove_gappy_sequences) == 'yes':
37 #if str($remove_gappy_sequences) == 'yes': 37 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
38 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 38 #set trim_type = $trim_type_cond.trim_type
39 #set trim_type = $trim_type_cond.trim_type 39 #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming):
40 #if str($trim_type) == 'gap_trimming' and str($trim_type_cond.gap_trimming): 40 --gap_trimming $trim_type_cond.gap_trimming
41 --gap_trimming $trim_type_cond.gap_trimming 41 #else:
42 #else: 42 ## str($trim_type) == 'automated_trimming'
43 ## str($trim_type) == 'automated_trimming' 43 --automated_trimming 'true'
44 --automated_trimming 'true' 44 #end if
45 #end if 45 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond
46 #set remove_sequences_with_gaps_cond = $remove_gappy_sequences_cond.remove_sequences_with_gaps_cond 46 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps
47 #set remove_sequences_with_gaps = $remove_sequences_with_gaps_cond.remove_sequences_with_gaps 47 #if str($remove_sequences_with_gaps) == 'yes':
48 #if str($remove_sequences_with_gaps) == 'yes': 48 #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of):
49 #if str($remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of): 49 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of
50 --remove_sequences $remove_sequences_with_gaps_cond.remove_sequences_with_gaps_of 50 #end if
51 #end if 51 #if str($remove_sequences_with_gaps_cond.iterative_realignment):
52 #if str($remove_sequences_with_gaps_cond.iterative_realignment): 52 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
53 --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment 53 #end if
54 #end if 54 #if $output_codon_alignments:
55 #if $output_codon_alignments: 55 --output '$output_aln_filtered_ca'
56 --output '$output_aln_filtered_ca' 56 --output_dir '$output_aln_filtered_ca.files_path'
57 --output_dir '$output_aln_filtered_ca.files_path' 57 #else:
58 #else: 58 --output '$output_aln_filtered'
59 --output '$output_aln_filtered' 59 --output_dir '$output_aln_filtered.files_path'
60 --output_dir '$output_aln_filtered.files_path' 60 #end if
61 #end if 61 #else:
62 #else: 62 #if $output_codon_alignments:
63 #if $output_codon_alignments: 63 --output '$output_aln_trimmed_ca'
64 --output '$output_aln_trimmed_ca' 64 --output_dir '$output_aln_trimmed_ca.files_path'
65 --output_dir '$output_aln_trimmed_ca.files_path' 65 #else:
66 #else: 66 --output '$output_aln_trimmed'
67 --output '$output_aln_trimmed' 67 --output_dir '$output_aln_trimmed.files_path'
68 --output_dir '$output_aln_trimmed.files_path' 68 #end if
69 #end if 69 #end if
70 #end if 70 #else:
71 #else: 71 #if $output_codon_alignments:
72 #if $output_codon_alignments: 72 --output '$output_aln_ca'
73 --output '$output_aln_ca' 73 --output_dir '$output_aln_ca.files_path'
74 --output_dir '$output_aln_ca.files_path' 74 #else:
75 #else: 75 --output '$output_aln'
76 --output '$output_aln' 76 --output_dir '$output_aln.files_path'
77 --output_dir '$output_aln.files_path' 77 #end if
78 #end if 78 #end if
79 #end if 79 ]]></command>
80 ]]>
81 </command>
82 <inputs> 80 <inputs>
83 <conditional name="input_format_cond"> 81 <conditional name="input_format_cond">
84 <param name="input_format" type="select" label="Classified orthogroup fasta files"> 82 <param name="input_format" type="select" label="Classified orthogroup fasta files">
85 <option value="ptortho">Proteins orthogroup fasta files</option> 83 <option value="ptortho">Proteins orthogroup fasta files</option>
86 <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option> 84 <option value="ptorthocs">Protein and coding sequences orthogroup fasta files</option>