Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 82:7d07e0ebe8c9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Wed, 22 Mar 2017 14:47:52 -0400
parents e528feaa44bd
children f0f02b73d5fe
comparison
equal deleted inserted replaced
81:3296048d5ea0 82:7d07e0ebe8c9
22 #end if 22 #end if
23 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond 23 #set phylogenetic_trees_cond = $options_type_cond.phylogenetic_trees_cond
24 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees 24 #set phylogenetic_trees = $phylogenetic_trees_cond.phylogenetic_trees
25 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond 25 #set remove_gappy_sequences_cond = $options_type_cond.remove_gappy_sequences_cond
26 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences 26 #set remove_gappy_sequences = $remove_gappy_sequences_cond.remove_gappy_sequences
27 #if str(input_format) == 'ptortho':
28 #set sequence_type = 'protein'
29 #else:
30 #set sequence_type = $phylogenetic_trees_cond.sequence_type
31 #set orthogroup_fna = $input_format_cond.orthogroup_fna
32 #end if
27 #end if 33 #end if
28 34
29 python $__tool_directory__/phylogenomics_analysis.py 35 python $__tool_directory__/phylogenomics_analysis.py
30 --num_threads \${GALAXY_SLOTS:-4} 36 --num_threads \${GALAXY_SLOTS:-4}
31 #if str($input_format) == 'ptortho': 37 #if str($input_format) == 'ptortho':
32 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path' 38 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
33 #else: 39 #else:
34 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path' 40 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
35 --orthogroup_fna 'true' 41 #if str($orthogroup_fna) == 'yes':
42 --orthogroup_fna 'true'
43 #end if
36 #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments 44 #set multiple_codon_alignments = $input_format_cond.multiple_codon_alignments
37 #if str($multiple_codon_alignments) == 'yes': 45 #if str($multiple_codon_alignments) == 'yes':
38 --codon_alignments 'true' 46 --codon_alignments 'true'
39 #end if 47 #end if
40 #end if 48 #end if
65 #end if 73 #end if
66 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates 74 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
67 #end if 75 #end if
68 --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size 76 --max_orthogroup_size $options_type_cond.phylogenetic_trees_cond.max_orthogroup_size
69 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size 77 --min_orthogroup_size $options_type_cond.phylogenetic_trees_cond.min_orthogroup_size
70 #if str($input_format) == 'ptortho': 78 --sequence_type $sequence_type
71 --sequence_type 'protein'
72 #else:
73 --sequence_type $phylogenetic_trees_cond.sequence_type
74 #end if
75 #end if 79 #end if
76 80
77 #if str($remove_gappy_sequences) == 'yes': 81 #if str($remove_gappy_sequences) == 'yes':
78 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond 82 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
79 #set trim_type = $trim_type_cond.trim_type 83 #set trim_type = $trim_type_cond.trim_type
128 </when> 132 </when>
129 </conditional> 133 </conditional>
130 </when> 134 </when>
131 <when value="ptorthocs"> 135 <when value="ptorthocs">
132 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" /> 136 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" />
137 <expand macro="param_orthogroup_fna" />
133 <expand macro="param_scaffold" /> 138 <expand macro="param_scaffold" />
134 <expand macro="param_method" /> 139 <expand macro="param_method" />
135 <conditional name="options_type_cond"> 140 <conditional name="options_type_cond">
136 <expand macro="param_options_type" /> 141 <expand macro="param_options_type" />
137 <when value="basic" /> 142 <when value="basic" />