Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 4:b78f5b0d0805 draft

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author greg
date Tue, 11 Apr 2017 13:13:53 -0400
parents 09a1b1b5aa0d
children 0e55cec5ec6b
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3:09a1b1b5aa0d 4:b78f5b0d0805
17 #end if 17 #end if
18 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates 18 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
19 #end if 19 #end if
20 20
21 python $__tool_directory__/gene_family_phylogeny_builder.py 21 python $__tool_directory__/gene_family_phylogeny_builder.py
22 --orthogroup_aln '$input_aln.extra_files_path' 22 #if str($input_format) == 'ptalign':
23 --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path'
24 --alignment_type 'aln'
25 --sequence_type 'protein'
26 #else if str($input_format) == 'ptalignca':
27 --orthogroup_aln '$input_format_cond.input_ptalignca.extra_files_path'
28 --alignment_type 'aln'
29 --sequence_type $input_format_cond.sequence_type
30 #else if str($input_format) == 'ptalignfiltered':
31 --orthogroup_aln '$input_format_cond.input_ptalignfiltered.extra_files_path'
32 --alignment_type 'filter'
33 --sequence_type 'protein'
34 #else if str($input_format) == 'ptalignfilteredca':
35 --orthogroup_aln '$input_format_cond.input_ptalignfilteredca.extra_files_path'
36 --alignment_type 'filter'
37 --sequence_type $input_format_cond.sequence_type
38 #else if str($input_format) == 'ptaligntrimmed':
39 --orthogroup_aln '$input_format_cond.input_ptaligntrimmed.extra_files_path'
40 --alignment_type 'trim'
41 --sequence_type 'protein'
42 #else if str($input_format) == 'ptaligntrimmedca':
43 --orthogroup_aln '$input_format_cond.input_ptaligntrimmedca.extra_files_path'
44 --alignment_type 'trim'
45 --sequence_type $input_format_cond.sequence_type
46 #end if
23 --scaffold '$scaffold.fields.path' 47 --scaffold '$scaffold.fields.path'
24 --config_dir '$scaffold.fields.path' 48 --config_dir '$scaffold.fields.path'
25 --method $method 49 --method $method
26 --tree_inference $tree_inference 50 --tree_inference $tree_inference
27 #if str($tree_inference) == 'raxml': 51 #if str($tree_inference) == 'raxml':
33 --bootstrap_replicates $bootstrap_replicates 57 --bootstrap_replicates $bootstrap_replicates
34 #end if 58 #end if
35 --min_orthogroup_size $min_orthogroup_size 59 --min_orthogroup_size $min_orthogroup_size
36 --max_orthogroup_size $max_orthogroup_size 60 --max_orthogroup_size $max_orthogroup_size
37 --num_threads \${GALAXY_SLOTS:-4} 61 --num_threads \${GALAXY_SLOTS:-4}
38 #if str($input_format) == 'ptalign':
39 --alignment_type 'aln'
40 --sequence_type 'protein'
41 #else if str($input_format) == 'ptalignca':
42 --alignment_type 'aln'
43 --sequence_type $input_format_cond.sequence_type
44 #else if str($input_format) == 'ptalignfiltered':
45 --alignment_type 'filter'
46 --sequence_type 'protein'
47 #else if str($input_format) == 'ptalignfilteredca':
48 --alignment_type 'filter'
49 --sequence_type $input_format_cond.sequence_type
50 #else if str($input_format) == 'ptaligntrimmed':
51 --alignment_type 'trim'
52 --sequence_type 'protein'
53 #else if str($input_format) == 'ptaligntrimmedca':
54 --alignment_type 'trim'
55 --sequence_type $input_format_cond.sequence_type
56 #end if
57 --output '$output_pttree' 62 --output '$output_pttree'
58 --output_dir '$output_pttree.files_path' 63 --output_dir '$output_pttree.files_path'
59 ]]> 64 ]]>
60 </command> 65 </command>
61 <inputs> 66 <inputs>