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comparison gene_family_phylogeny_builder.xml @ 6:a7867769a706 draft

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author greg
date Mon, 30 Oct 2017 09:53:46 -0400
parents 34ca28db0a5d
children c088c185f63f
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5:34ca28db0a5d 6:a7867769a706
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 <requirements>
7 <requirement type="package" version="1.0.3">plant_tribes_gene_family_phylogeny_builder</requirement>
8 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
8 #set input_format = $input_format_cond.input_format 10 #set input_dir = 'input_dir'
9 #set tree_inference = $tree_inference_cond.tree_inference 11 #set tree_inference = $tree_inference_cond.tree_inference
10 #if str($tree_inference) == 'raxml': 12 #if str($tree_inference) == 'raxml':
13 #set scaffold = $tree_inference_cond.scaffold
14 #set method = $tree_inference_cond.method
11 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond 15 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
12 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file 16 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
13 #if str($rooting_order_file) == 'yes': 17 #if str($rooting_order_file) == 'yes':
14 #set rooting_order = $rooting_order_file_cond.rooting_order 18 #set rooting_order = $rooting_order_file_cond.rooting_order
15 #end if 19 #end if
16 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates 20 #set bootstrap_replicates = $tree_inference_cond.bootstrap_replicates
17 #end if 21 #end if
18 22 mkdir $input_dir &&
23 #for $i in $input:
24 #set filename = $i.file_name
25 #set name = $i.name
26 ln -s $filename $input_dir/$name &&
27 #end for
19 GeneFamilyPhylogenyBuilder 28 GeneFamilyPhylogenyBuilder
20 #if str($input_format) == 'ptalign': 29 --orthogroup_aln '$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'
46 --config_dir '$scaffold.fields.path'
47 --method $method
48 --tree_inference $tree_inference 30 --tree_inference $tree_inference
49 #if str($tree_inference) == 'raxml': 31 #if str($tree_inference) == 'raxml':
32 --scaffold '$scaffold.fields.path'
33 --config_dir '$scaffold.fields.path'
34 --method $method
50 #if str($rooting_order_file) == 'yes': 35 #if str($rooting_order_file) == 'yes':
51 --rooting_order '$rooting_order' 36 --rooting_order '$rooting_order'
52 ## No else block needed here because the default rooting_order 37 ## No else block needed here because the default rooting_order
53 ## configuration will be used if the --rooting_order flag is missing. 38 ## configuration will be used if the --rooting_order flag is missing.
54 #end if 39 #end if
55 --bootstrap_replicates $bootstrap_replicates 40 --bootstrap_replicates $bootstrap_replicates
56 #end if 41 #end if
57 --min_orthogroup_size $min_orthogroup_size 42 --min_orthogroup_size $min_orthogroup_size
58 --max_orthogroup_size $max_orthogroup_size 43 --max_orthogroup_size $max_orthogroup_size
59 --num_threads \${GALAXY_SLOTS:-4} 44 --num_threads \${GALAXY_SLOTS:-4}
45 &>proc.log
60 ]]></command> 46 ]]></command>
61 <inputs> 47 <inputs>
62 <conditional name="input_format_cond"> 48 <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" />
106 <expand macro="param_method" />
107 <conditional name="tree_inference_cond"> 49 <conditional name="tree_inference_cond">
108 <param name="tree_inference" type="select" label="Phylogenetic inference method"> 50 <param name="tree_inference" type="select" label="Phylogenetic inference method">
109 <option value="raxml" selected="true">RAxML</option> 51 <option value="raxml" selected="true">RAxML</option>
110 <option value="fasttree">FastTree</option> 52 <option value="fasttree">FastTree</option>
111 </param> 53 </param>
112 <when value="raxml"> 54 <when value="raxml">
55 <expand macro="param_scaffold" />
56 <expand macro="param_method" />
113 <conditional name="rooting_order_file_cond"> 57 <conditional name="rooting_order_file_cond">
114 <param name="rooting_order_file" type="select" label="Rooting order configuration"> 58 <param name="rooting_order_file" type="select" label="Rooting order configuration">
115 <option value="no" selected="true">No</option> 59 <option value="no" selected="true">No</option>
116 <option value="yes">Yes</option> 60 <option value="yes">Yes</option>
117 </param> 61 </param>
135 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter> 79 <filter>tree_inference_cond['tree_inference'] == 'raxml'</filter>
136 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" /> 80 <discover_datasets pattern="__name__" directory="geneFamilyPhylogenies_dir/phylip_aln" format="phylip" />
137 </collection> 81 </collection>
138 </outputs> 82 </outputs>
139 <tests> 83 <tests>
140 <!-- Test framework does not currently support inputs whose associated extra_files_path contains files to be analyzed.
141 <test> 84 <test>
85 <param name="input">
86 <collection type="list">
87 <element name="3722.faa.aln" value="3722.faa.aln"/>
88 </collection>
89 </param>
90 <param name="tree_inference" value="fasttree"/>
91 <output_collection name="tree" type="list">
92 <element name="3722.faa.aln.tree" file="3722.faa.aln.tree" ftype="nhx"/>
93 </output_collection>
142 </test> 94 </test>
143 -->
144 </tests> 95 </tests>
145 <help> 96 <help>
146 This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary 97 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 98 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. 99 multiple sequence alignments produced by the GeneFamilyAligner tool.
150 ----- 101 -----
151 102
152 **Required options** 103 **Required options**
153 104
154 * **Orthogroup alignments** - orthogroup alignment fasta files produced by the GeneFamilyAligner tool selected from your history. Depending on how the GeneFamilyAligner tool was executed, these could either be pre-processed alignments, trimmed alignments or both trimmed and filtered alignments. 105 * **Orthogroup alignments** - orthogroup alignment fasta files produced by the GeneFamilyAligner tool selected from your history. Depending on how the GeneFamilyAligner tool was executed, these could either be pre-processed alignments, trimmed alignments or both trimmed and filtered alignments.
155 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Download Data Manager tool.
156 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
157 * **Phylogenetic inference method** - method for estimating orthogroup maximum likelihood (ML) phylogenetic trees. PlantTribes estimates ML phylogenetic trees using either RAxML or FastTree algorithms. 106 * **Phylogenetic inference method** - method for estimating orthogroup maximum likelihood (ML) phylogenetic trees. PlantTribes estimates ML phylogenetic trees using either RAxML or FastTree algorithms.
107
108 - **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Download Data Manager tool. This is used only if RAxML is selected as the phylogenetic inference method.
109 - **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool. This is used only if RAxML is selected as the phylogenetic inference method.
158 110
159 **Other options** 111 **Other options**
160 112
161 * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML. Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub `repository`_. Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected. 113 * **Rooting order configuration** - select 'Yes' to enable selection of a rooting order configuration file for RAxML. Scaffold configuration templates (.rootingOrder.config) of how to customize the RAxML ML tree rooting order can be found in the scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and is also available at the PlantTribes GitHub `repository`_. Phylogenetic tree rooting order settings shown in these templates are used as defaults if 'No' is selected.
162 * **Bootstrap replicates** - number of bootstrap replicates for RAxML to conduct a rapid bootstrap analysis and search for the best-scoring ML tree (default = 100). 114 * **Bootstrap replicates** - number of bootstrap replicates for RAxML to conduct a rapid bootstrap analysis and search for the best-scoring ML tree (default = 100).
163 * **Maximum orthogroup size** - maximum number of sequences allowed in orthogroup alignments (default = 100). 115 * **Maximum orthogroup size** - maximum number of sequences allowed in orthogroup alignments (default = 100).
164 * **Minimum orthogroup size** - minimum number of sequences allowed in orthogroup alignments (default = 4). 116 * **Minimum orthogroup size** - minimum number of sequences allowed in orthogroup alignments (default = 4).
165 * **Output additional directory of phylogenetic tree files** - selecting 'Yes' will produce an additional output that has an associated directory of files that are copies of the elements of the phylogenetic trees output dataset collection (this output will be used for future downstream tools).
166 117
167 .. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config 118 .. _repository: https://github.com/dePamphilis/PlantTribes/tree/master/config
168 119
169 </help> 120 </help>
170 <citations> 121 <citations>