0
+ − 1 <?xml version='1.0' encoding='UTF-8'?>
+ − 2 <macros>
+ − 3 <token name="@WRAPPER_VERSION@">1.0</token>
+ − 4 <xml name="requirements_assembly_post_processor">
+ − 5 <requirements>
+ − 6 <requirement type="package" version="1.0.0">plant_tribes_assembly_post_processor</requirement>
+ − 7 </requirements>
+ − 8 </xml>
+ − 9 <xml name="requirements_gene_family_aligner">
+ − 10 <requirements>
+ − 11 <requirement type="package" version="1.0.0">plant_tribes_gene_family_aligner</requirement>
+ − 12 </requirements>
+ − 13 </xml>
+ − 14 <xml name="requirements_gene_family_classifier">
+ − 15 <requirements>
+ − 16 <requirement type="package" version="1.0.0">plant_tribes_gene_family_classifier</requirement>
+ − 17 </requirements>
+ − 18 </xml>
+ − 19 <xml name="requirements_gene_family_integrator">
+ − 20 <requirements>
+ − 21 <requirement type="package" version="1.0.0">plant_tribes_gene_family_integrator</requirement>
+ − 22 </requirements>
+ − 23 </xml>
+ − 24 <xml name="requirements_kaks_analysis">
+ − 25 <requirements>
+ − 26 <requirement type="package" version="1.0.0">plant_tribes_kaks_analysis</requirement>
+ − 27 </requirements>
+ − 28 </xml>
+ − 29 <xml name="requirements_ks_distribution">
+ − 30 <requirements>
+ − 31 <requirement type="package" version="1.3.0">r-optparse</requirement>
+ − 32 </requirements>
+ − 33 </xml>
+ − 34 <xml name="requirements_gene_family_phylogeny_builder">
+ − 35 <requirements>
+ − 36 <requirement type="package" version="1.0.0">plant_tribes_gene_family_phylogeny_builder</requirement>
+ − 37 </requirements>
+ − 38 </xml>
+ − 39 <xml name="param_codon_alignments">
+ − 40 <param name="codon_alignments" type="select" label="Codon alignments">
+ − 41 <option value="yes" selected="true">Yes</option>
+ − 42 <option value="no">No</option>
+ − 43 </param>
+ − 44 </xml>
+ − 45 <xml name="param_method">
+ − 46 <param name="method" type="select" label="Protein clustering method">
+ − 47 <option value="gfam" selected="true">GFam</option>
+ − 48 <option value="orthofinder">OrthoFinder</option>
+ − 49 <option value="orthomcl">OrthoMCL</option>
+ − 50 </param>
+ − 51 </xml>
+ − 52 <xml name="param_options_type">
+ − 53 <param name="options_type" type="select" label="Options Configuration">
+ − 54 <option value="basic" selected="true">Basic</option>
+ − 55 <option value="advanced">Advanced</option>
+ − 56 </param>
+ − 57 </xml>
+ − 58 <xml name="param_orthogroup_fna">
+ − 59 <param name="orthogroup_fna" type="select" label="Orthogroups coding sequences">
+ − 60 <option value="yes" selected="true">Yes</option>
+ − 61 <option value="no">No</option>
+ − 62 </param>
+ − 63 </xml>
+ − 64 <xml name="param_scaffold">
+ − 65 <param name="scaffold" type="select" label="Gene family scaffold">
+ − 66 <options from_data_table="plant_tribes_scaffolds" />
+ − 67 <validator type="no_options" message="No PlantTribes scaffolds are available. Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
+ − 68 </param>
+ − 69 </xml>
+ − 70 <xml name="param_sequence_type">
+ − 71 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
+ − 72 <option value="protein" selected="true">Amino acid based</option>
+ − 73 <option value="dna">Nucleotide based</option>
+ − 74 </param>
+ − 75 </xml>
+ − 76 <xml name="cond_alignment_method">
+ − 77 <conditional name="alignment_method_cond">
+ − 78 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
+ − 79 <option value="mafft" selected="true">MAFFT</option>
+ − 80 <option value="pasta">PASTA</option>
+ − 81 </param>
+ − 82 <when value="mafft" />
+ − 83 <when value="pasta">
+ − 84 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
+ − 85 </when>
+ − 86 </conditional>
+ − 87 </xml>
+ − 88 <xml name="cond_remove_gappy_sequences">
+ − 89 <conditional name="remove_gappy_sequences_cond">
+ − 90 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
+ − 91 <option value="no" selected="true">No</option>
+ − 92 <option value="yes">Yes</option>
+ − 93 </param>
+ − 94 <when value="no" />
+ − 95 <when value="yes">
+ − 96 <conditional name="trim_type_cond">
+ − 97 <param name="trim_type" type="select" label="Trimming method">
+ − 98 <option value="gap_trimming" selected="true">Gap score based trimming</option>
+ − 99 <option value="automated_trimming">Automated heuristic trimming</option>
+ − 100 </param>
+ − 101 <when value="gap_trimming">
+ − 102 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
+ − 103 </when>
+ − 104 <when value="automated_trimming" />
+ − 105 </conditional>
+ − 106 <conditional name="remove_sequences_with_gaps_cond">
+ − 107 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences">
+ − 108 <option value="no" selected="true">No</option>
+ − 109 <option value="yes">Yes</option>
+ − 110 </param>
+ − 111 <when value="no" />
+ − 112 <when value="yes">
+ − 113 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
+ − 114 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
+ − 115 </when>
+ − 116 </conditional>
+ − 117 </when>
+ − 118 </conditional>
+ − 119 </xml>
+ − 120 <xml name="citation1">
+ − 121 <citation type="bibtex">
+ − 122 @misc{None,
+ − 123 journal = {None},
+ − 124 author = {1. Wafula EK},
+ − 125 title = {Manuscript in preparation},
+ − 126 year = {None},
+ − 127 url = {https://github.com/dePamphilis/PlantTribes},}
+ − 128 </citation>
+ − 129 </xml>
+ − 130 </macros>
