Mercurial > repos > greg > plant_tribes_gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 1:f5ae6c86f75f draft

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author greg
date Tue, 01 Aug 2017 14:26:25 -0400
parents 7000422fbaff
children a0def395ad14
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0:7000422fbaff 1:f5ae6c86f75f
14 #set rooting_order = $rooting_order_file_cond.rooting_order 14 #set rooting_order = $rooting_order_file_cond.rooting_order
15 #end if 15 #end if
16 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates 16 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
17 #end if 17 #end if
18 18
19 python $__tool_directory__/gene_family_phylogeny_builder.py 19 python '$__tool_directory__/gene_family_phylogeny_builder.py'
20 #if str($input_format) == 'ptalign': 20 #if str($input_format) == 'ptalign':
21 --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path' 21 --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path'
22 --alignment_type 'aln' 22 --alignment_type aln
23 --sequence_type 'protein' 23 --sequence_type protein
24 #else if str($input_format) == 'ptalignca': 24 #else if str($input_format) == 'ptalignca':
25 --orthogroup_aln '$input_format_cond.input_ptalignca.extra_files_path' 25 --orthogroup_aln '$input_format_cond.input_ptalignca.extra_files_path'
26 --alignment_type 'aln' 26 --alignment_type aln
27 --sequence_type $input_format_cond.sequence_type 27 --sequence_type $input_format_cond.sequence_type
28 #else if str($input_format) == 'ptalignfiltered': 28 #else if str($input_format) == 'ptalignfiltered':
29 --orthogroup_aln '$input_format_cond.input_ptalignfiltered.extra_files_path' 29 --orthogroup_aln '$input_format_cond.input_ptalignfiltered.extra_files_path'
30 --alignment_type 'filter' 30 --alignment_type filter
31 --sequence_type 'protein' 31 --sequence_type protein
32 #else if str($input_format) == 'ptalignfilteredca': 32 #else if str($input_format) == 'ptalignfilteredca':
33 --orthogroup_aln '$input_format_cond.input_ptalignfilteredca.extra_files_path' 33 --orthogroup_aln '$input_format_cond.input_ptalignfilteredca.extra_files_path'
34 --alignment_type 'filter' 34 --alignment_type filter
35 --sequence_type $input_format_cond.sequence_type 35 --sequence_type $input_format_cond.sequence_type
36 #else if str($input_format) == 'ptaligntrimmed': 36 #else if str($input_format) == 'ptaligntrimmed':
37 --orthogroup_aln '$input_format_cond.input_ptaligntrimmed.extra_files_path' 37 --orthogroup_aln '$input_format_cond.input_ptaligntrimmed.extra_files_path'
38 --alignment_type 'trim' 38 --alignment_type trim
39 --sequence_type 'protein' 39 --sequence_type protein
40 #else if str($input_format) == 'ptaligntrimmedca': 40 #else if str($input_format) == 'ptaligntrimmedca':
41 --orthogroup_aln '$input_format_cond.input_ptaligntrimmedca.extra_files_path' 41 --orthogroup_aln '$input_format_cond.input_ptaligntrimmedca.extra_files_path'
42 --alignment_type 'trim' 42 --alignment_type trim
43 --sequence_type $input_format_cond.sequence_type 43 --sequence_type $input_format_cond.sequence_type
44 #end if 44 #end if
45 --scaffold '$scaffold.fields.path' 45 --scaffold '$scaffold.fields.path'
46 --config_dir '$scaffold.fields.path' 46 --config_dir '$scaffold.fields.path'
47 --method $method 47 --method $method