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