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comparison gene_family_phylogeny_builder.xml @ 46:8262754dc5f9 draft

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author greg
date Fri, 08 Sep 2017 10:05:30 -0400
parents 97a298d2fc36
children 22d6092baa99
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45:5873a9420e03 46:8262754dc5f9
1 <tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.2.1"> 1 <tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.3.0">
2 <description>builds phylogenetic trees of aligned orthologous gene family clusters</description> 2 <description>builds phylogenetic trees of aligned 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_phylogeny_builder" /> 6 <expand macro="requirements_gene_family_phylogeny_builder" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #set input_format = $input_format_cond.input_format 8 #set input_dir = 'input_dir'
9 #set tree_inference = $tree_inference_cond.tree_inference 9 #set tree_inference = $tree_inference_cond.tree_inference
10 #if str($tree_inference) == 'raxml': 10 #if str($tree_inference) == 'raxml':
11 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond 11 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
12 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file 12 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
13 #if str($rooting_order_file) == 'yes': 13 #if str($rooting_order_file) == 'yes':
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 mkdir $input_dir &&
19 #for $dce in $input:
20 #set filename = $dce.element_object.filename
21 ln -s $filename $input_dir
22 #end for
19 GeneFamilyPhylogenyBuilder 23 GeneFamilyPhylogenyBuilder
20 #if str($input_format) == 'ptalign': 24 --orthogroup_aln '$input_dir'
21 --orthogroup_aln '$input_format_cond.input_ptalign.extra_files_path'
22 --alignment_type aln
23 --sequence_type protein
24 #else if str($input_format) == 'ptalignca':
25 --orthogroup_aln '$input_format_cond.input_ptalignca.extra_files_path'
26 --alignment_type aln
27 --sequence_type $input_format_cond.sequence_type
28 #else if str($input_format) == 'ptalignfiltered':
29 --orthogroup_aln '$input_format_cond.input_ptalignfiltered.extra_files_path'
30 --alignment_type filter
31 --sequence_type protein
32 #else if str($input_format) == 'ptalignfilteredca':
33 --orthogroup_aln '$input_format_cond.input_ptalignfilteredca.extra_files_path'
34 --alignment_type filter
35 --sequence_type $input_format_cond.sequence_type
36 #else if str($input_format) == 'ptaligntrimmed':
37 --orthogroup_aln '$input_format_cond.input_ptaligntrimmed.extra_files_path'
38 --alignment_type trim
39 --sequence_type protein
40 #else if str($input_format) == 'ptaligntrimmedca':
41 --orthogroup_aln '$input_format_cond.input_ptaligntrimmedca.extra_files_path'
42 --alignment_type trim
43 --sequence_type $input_format_cond.sequence_type
44 #end if
45 --scaffold '$scaffold.fields.path' 25 --scaffold '$scaffold.fields.path'
46 --config_dir '$scaffold.fields.path' 26 --config_dir '$scaffold.fields.path'
47 --method $method 27 --method $method
48 --tree_inference $tree_inference 28 --tree_inference $tree_inference
49 #if str($tree_inference) == 'raxml': 29 #if str($tree_inference) == 'raxml':
57 --min_orthogroup_size $min_orthogroup_size 37 --min_orthogroup_size $min_orthogroup_size
58 --max_orthogroup_size $max_orthogroup_size 38 --max_orthogroup_size $max_orthogroup_size
59 --num_threads \${GALAXY_SLOTS:-4} 39 --num_threads \${GALAXY_SLOTS:-4}
60 ]]></command> 40 ]]></command>
61 <inputs> 41 <inputs>
62 <conditional name="input_format_cond"> 42 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup alignments" />
63 <param name="input_format" type="select" label="Orthogroup alignments">
64 <option value="ptalign">Proteins orthogroup alignments</option>
65 <option value="ptalignca">Protein and coding sequences orthogroup alignments</option>
66 <option value="ptalignfiltered">Filtered proteins orthogroup alignments</option>
67 <option value="ptalignfilteredca">Filtered protein and coding sequences orthogroup alignments</option>
68 <option value="ptaligntrimmed">Trimmed proteins orthogroup alignments</option>
69 <option value="ptaligntrimmedca">Trimmed protein and coding sequences orthogroup alignments</option>
70 </param>
71 <when value="ptalign">
72 <param name="input_ptalign" format="ptalign" type="data" label="Proteins orthogroup alignments">
73 <validator type="empty_extra_files_path" />
74 </param>
75 </when>
76 <when value="ptalignca">
77 <param name="input_ptalignca" format="ptalignca" type="data" label="Protein and coding sequences orthogroup alignments">
78 <validator type="empty_extra_files_path" />
79 </param>
80 <expand macro="param_sequence_type" />
81 </when>
82 <when value="ptalignfiltered">
83 <param name="input_ptalignfiltered" format="ptalignfiltered" type="data" label="Filtered proteins orthogroup alignments">
84 <validator type="empty_extra_files_path" />
85 </param>
86 </when>
87 <when value="ptalignfilteredca">
88 <param name="input_ptalignfilteredca" format="ptalignfilteredca" type="data" label="Filtered protein and coding sequences orthogroup alignments">
89 <validator type="empty_extra_files_path" />
90 </param>
91 <expand macro="param_sequence_type" />
92 </when>
93 <when value="ptaligntrimmed">
94 <param name="input_ptaligntrimmed" format="ptaligntrimmed" type="data" label="Trimmed proteins orthogroup alignments">
95 <validator type="empty_extra_files_path" />
96 </param>
97 </when>
98 <when value="ptaligntrimmedca">
99 <param name="input_ptaligntrimmedca" format="ptaligntrimmedca" type="data" label="Trimmed protein and coding sequences orthogroup alignments">
100 <validator type="empty_extra_files_path" />
101 </param>
102 <expand macro="param_sequence_type" />
103 </when>
104 </conditional>
105 <expand macro="param_scaffold" /> 43 <expand macro="param_scaffold" />
106 <expand macro="param_method" /> 44 <expand macro="param_method" />
107 <conditional name="tree_inference_cond"> 45 <conditional name="tree_inference_cond">
108 <param name="tree_inference" type="select" label="Phylogenetic inference method"> 46 <param name="tree_inference" type="select" label="Phylogenetic inference method">
109 <option value="raxml" selected="true">RAxML</option> 47 <option value="raxml" selected="true">RAxML</option>
135 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter> 73 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
136 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" /> 74 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" />
137 </collection> 75 </collection>
138 </outputs> 76 </outputs>
139 <tests> 77 <tests>
140 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
141 <test> 78 <test>
142 </test> 79 </test>
143 -->
144 </tests> 80 </tests>
145 <help> 81 <help>
146 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary 82 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary
147 analyses of genome-scale gene families and transcriptomes. This tool performs gene family phylogenetic inference of 83 analyses of genome-scale gene families and transcriptomes. This tool performs gene family phylogenetic inference of
148 multiple sequence alignments produced by the GeneFamilyAligner tool. 84 multiple sequence alignments produced by the GeneFamilyAligner tool.