Mercurial > repos > greg > gene_family_phylogeny_builder

comparison gene_family_phylogeny_builder.xml @ 54:eef0f4704dca draft

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author greg
date Wed, 25 Oct 2017 11:30:45 -0400
parents 24774c743d31
children 178971bba68f
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53:24774c743d31 54:eef0f4704dca
40 --bootstrap_replicates $bootstrap_replicates 40 --bootstrap_replicates $bootstrap_replicates
41 #end if 41 #end if
42 --min_orthogroup_size $min_orthogroup_size 42 --min_orthogroup_size $min_orthogroup_size
43 --max_orthogroup_size $max_orthogroup_size 43 --max_orthogroup_size $max_orthogroup_size
44 --num_threads \${GALAXY_SLOTS:-4} 44 --num_threads \${GALAXY_SLOTS:-4}
45 &>proc.log
45 ]]></command> 46 ]]></command>
46 <inputs> 47 <inputs>
47 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup alignments" /> 48 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup alignments" />
48 <conditional name="tree_inference_cond"> 49 <conditional name="tree_inference_cond">
49 <param name="tree_inference" type="select" label="Phylogenetic inference method"> 50 <param name="tree_inference" type="select" label="Phylogenetic inference method">
84 <param name="input"> 85 <param name="input">
85 <collection type="list"> 86 <collection type="list">
86 <element name="3722.faa.aln" value="3722.faa.aln"/> 87 <element name="3722.faa.aln" value="3722.faa.aln"/>
87 </collection> 88 </collection>
88 </param> 89 </param>
89 <param name="tree_inference" value="raxml"/> 90 <param name="tree_inference" value="fasttree"/>
90 <param name="scaffold" value="22Gv1.1"/>
91 <param name="method" value="orthomcl"/>
92 <output_collection name="tree" type="list"> 91 <output_collection name="tree" type="list">
93 <element name="3722.faa.aln.tree" file="3722.faa.aln.tree" ftype="nhx"/> 92 <element name="3722.faa.aln.tree" file="3722.faa.aln.tree" ftype="nhx"/>
94 </output_collection> 93 </output_collection>
95 </test> 94 </test>
96 </tests> 95 </tests>
102 ----- 101 -----
103 102
104 **Required options** 103 **Required options**
105 104
106 * **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.
107 * **Gene family scaffold** - one of the PlantTribes gene family scaffolds installed into Galaxy by the PlantTribes Scaffold Download Data Manager tool.
108 * **Protein clustering method** - gene family scaffold protein clustering method as described in the AssemblyPostProcessor tool.
109 * **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.
110 110
111 **Other options** 111 **Other options**
112 112
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. 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.
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). 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).