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comparison gene_family_phylogeny_builder.xml @ 0:f4361d941aa3 draft

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author greg
date Tue, 11 Apr 2017 11:05:24 -0400
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1 <tool id="plant_tribes_gene_family_phylogeny_builder" name="GeneFamilyPhylogenyBuilder" version="@WRAPPER_VERSION@.0">
2 <description>builds gene family phylogenetic trees</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements_gene_family_phylogeny_builder" />
7 <expand macro="stdio" />
8 <command>
9 <![CDATA[
10 #set input_format = $input_format_cond.input_format
11 #set tree_inference_cond = $phylogenetic_trees_cond.tree_inference_cond
12 #set tree_inference = $tree_inference_cond.tree_inference
13 #if str($tree_inference) == 'raxml':
14 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
15 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
16 #if str($rooting_order_file) == 'yes':
17 #set rooting_order = $rooting_order_file_cond.rooting_order
18 #end if
19 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
20 #end if
21
22 python $__tool_directory__/gene_family_phylogeny_builder.py
23 --orthogroup_aln '$input_aln.extra_files_path'
24 --scaffold '$scaffold.fields.path'
25 --config_dir '$scaffold.fields.path'
26 --method $method
27 --tree_inference $tree_inference
28 #if str($tree_inference) == 'raxml':
29 #if str($rooting_order_file) == 'yes':
30 --rooting_order '$rooting_order'
31 ## No else block needed here because the default rooting_order
32 ## configuration will be used if the --rooting_order flag is missing.
33 #end if
34 --bootstrap_replicates $bootstrap_replicates
35 #end if
36 --min_orthogroup_size $min_orthogroup_size
37 --max_orthogroup_size $max_orthogroup_size
38 --num_threads \${GALAXY_SLOTS:-4}
39 #if str($input_format) == 'ptalign':
40 --alignment_type 'aln'
41 --sequence_type 'protein'
42 #else if str($input_format) == 'ptalignca':
43 --alignment_type 'aln'
44 --sequence_type $input_format_cond.sequence_type
45 #else if str($input_format) == 'ptalignfiltered':
46 --alignment_type 'filter'
47 --sequence_type 'protein'
48 #else if str($input_format) == 'ptalignfilteredca':
49 --alignment_type 'filter'
50 --sequence_type $input_format_cond.sequence_type
51 #else if str($input_format) == 'ptaligntrimmed':
52 --alignment_type 'trim'
53 --sequence_type 'protein'
54 #else if str($input_format) == 'ptaligntrimmedca':
55 --alignment_type 'trim'
56 --sequence_type $input_format_cond.sequence_type
57 #end if
58 --output '$output_pttree'
59 --output_dir '$output_pttree.files_path'
60 ]]>
61 </command>
62 <inputs>
63 <conditional name="input_format_cond">
64 <param name="input_format" type="select" label="Select type of data">
65 <option value="ptalign">Aligned gene family sequences</option>
66 <option value="ptalignca">Aligned gene family sequences with codon alignments</option>
67 <option value="ptalignfiltered">Filtered aligned gene family sequences</option>
68 <option value="ptalignfilteredca">Filtered aligned gene family sequences with codon alignments</option>
69 <option value="ptaligntrimmed">Trimmed aligned gene family sequences</option>
70 <option value="ptaligntrimmedca">Trimmed aligned gene family sequences with codon alignments</option>
71 </param>
72 <when value="ptalign">
73 <param name="input_ptalign" format="ptalign" type="data" label="Aligned gene family sequences">
74 <validator type="empty_files_path" />
75 </param>
76 </when>
77 <when value="ptalignca">
78 <param name="input_ptalignca" format="ptalignca" type="data" label="Aligned gene family sequences with codon alignments">
79 <validator type="empty_files_path" />
80 </param>
81 <expand macro="param_sequence_type" />
82 </when>
83 <when value="ptalignfiltered">
84 <param name="input_ptalignfiltered" format="ptalignfiltered" type="data" label="Filtered aligned gene family sequences">
85 <validator type="empty_files_path" />
86 </param>
87 </when>
88 <when value="ptalignfilteredca">
89 <param name="input_ptalignfilteredca" format="ptalignfilteredca" type="data" label="Filtered aligned gene family sequences with codon alignments">
90 <validator type="empty_files_path" />
91 </param>
92 <expand macro="param_sequence_type" />
93 </when>
94 <when value="ptaligntrimmed">
95 <param name="input_ptaligntrimmed" format="ptaligntrimmed" type="data" label="Trimmed aligned gene family sequences">
96 <validator type="empty_files_path" />
97 </param>
98 </when>
99 <when value="ptaligntrimmedca">
100 <param name="input_ptaligntrimmedca" format="ptaligntrimmedca" type="data" label="Trimmed aligned gene family sequences with codon alignments">
101 <validator type="empty_files_path" />
102 </param>
103 <expand macro="param_sequence_type" />
104 </when>
105 </conditional>
106 <expand macro="param_scaffold" />
107 <expand macro="param_method" />
108 <conditional name="tree_inference_cond">
109 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
110 <option value="raxml" selected="true">RAxML</option>
111 <option value="fasttree">FastTree</option>
112 </param>
113 <when value="raxml">
114 <conditional name="rooting_order_file_cond">
115 <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select No for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
116 <option value="no" selected="true">No</option>
117 <option value="yes">Yes</option>
118 </param>
119 <when value="no" />
120 <when value="yes">
121 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
122 </when>
123 </conditional>
124 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
125 </when>
126 <when value="fasttree" />
127 </conditional>
128 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
129 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
130 </inputs>
131 <outputs>
132 <data name="output_pttree" format="pttree" label="Gene family phylogenetic trees on ${on_string}" />
133 </outputs>
134 <tests>
135 <!-- Test framework does not currently support inputs whose associated files_path contains files to be analyzed.
136 <test>
137 </test>
138 -->
139 </tests>
140 <help>
141 This tool is one of the PlantTribes collection of automated modular analysis pipelines that utilize objective classifications of
142 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
143 analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
144 **GeneFamilyAligner** tool.
145
146 -----
147
148 **Required options**
149
150 **Other options**
151
152 </help>
153 <citations>
154 <expand macro="citation1" />
155 <expand macro="citations2to4" />
156 </citations>
157 </tool>