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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <macros>
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6
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3 <token name="@WRAPPER_VERSION@">0.8</token>
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0
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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="0.4">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="0.8">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="0.8">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="0.8">plant_tribes_gene_family_integrator</requirement>
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22 </requirements>
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23 </xml>
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5
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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="0.8">plant_tribes_kaks_analysis</requirement>
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27 </requirements>
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28 </xml>
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6
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29 <xml name="requirements_gene_family_phylogeny_builder">
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30 <requirements>
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31 <requirement type="package" version="0.8">plant_tribes_gene_family_phylogeny_builder</requirement>
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32 </requirements>
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33 </xml>
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0
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34 <xml name="stdio">
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35 <stdio>
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36 <exit_code range="1:"/>
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37 <exit_code range=":-1"/>
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38 <regex match="Error:"/>
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39 <regex match="Exception:"/>
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40 </stdio>
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41 </xml>
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42 <xml name="param_codon_alignments">
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5
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43 <param name="codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
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44 <option value="yes" selected="true">Yes</option>
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45 <option value="no">No</option>
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46 </param>
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47 </xml>
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48 <xml name="param_method">
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49 <param name="method" type="select" label="Protein clustering method">
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50 <option value="gfam" selected="true">GFam</option>
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51 <option value="orthofinder">OrthoFinder</option>
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52 <option value="orthomcl">OrthoMCL</option>
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53 </param>
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54 </xml>
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55 <xml name="param_options_type">
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56 <param name="options_type" type="select" label="Options Configuration">
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57 <option value="basic" selected="true">Basic</option>
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58 <option value="advanced">Advanced</option>
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59 </param>
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60 </xml>
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61 <xml name="param_orthogroup_fna">
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5
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62 <param name="orthogroup_fna" type="select" label="Process corresponding gene family classification orthogroups CDS fasta files?">
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0
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63 <option value="yes" selected="true">Yes</option>
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64 <option value="no">No</option>
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65 </param>
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66 </xml>
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67 <xml name="param_scaffold">
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68 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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69 <options from_data_table="plant_tribes_scaffolds" />
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70 <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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71 </param>
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72 </xml>
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14
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73 <xml name="param_sequence_type">
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74 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
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75 <option value="protein" selected="true">Amino acid based</option>
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76 <option value="dna">Nucleotide based</option>
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77 </param>
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78 </xml>
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0
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79 <xml name="cond_alignment_method">
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80 <conditional name="alignment_method_cond">
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1
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81 <param name="alignment_method" type="select" force_select="true" label="Select method for multiple sequence alignments">
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0
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82 <option value="mafft" selected="true">MAFFT algorithm</option>
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83 <option value="pasta">PASTA algorithm</option>
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84 </param>
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85 <when value="mafft" />
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86 <when value="pasta">
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87 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="Maximum number of iterations that the PASTA algorithm will execute" />
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88 </when>
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89 </conditional>
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90 </xml>
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91 <xml name="cond_remove_gappy_sequences">
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92 <conditional name="remove_gappy_sequences_cond">
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93 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
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94 <option value="no" selected="true">No</option>
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95 <option value="yes">Yes</option>
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96 </param>
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97 <when value="no" />
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98 <when value="yes">
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99 <conditional name="trim_type_cond">
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11
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100 <param name="trim_type" type="select" label="Select process used for trimming">
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101 <option value="gap_trimming" selected="true">Remove gappy sites in alignments (gap trimming)</option>
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102 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach (automated trimming)</option>
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0
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103 </param>
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104 <when value="gap_trimming">
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14
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105 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Remove sites in alignments with gaps of" />
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0
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106 </when>
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107 <when value="automated_trimming" />
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108 </conditional>
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109 <conditional name="remove_sequences_with_gaps_cond">
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110 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences with specified gaps?">
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111 <option value="no" selected="true">No</option>
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112 <option value="yes">Yes</option>
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113 </param>
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114 <when value="no" />
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115 <when value="yes">
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14
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116 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Remove sequences with gaps of" />
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117 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Maximum number of iterations" />
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0
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118 </when>
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119 </conditional>
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120 </when>
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121 </conditional>
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122 </xml>
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123 <xml name="citation1">
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124 <citation type="bibtex">
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125 @misc{None,
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126 journal = {None},
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127 author = {1. Wafula EK},
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128 title = {Manuscript in preparation},
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129 year = {None},
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130 url = {https://github.com/dePamphilis/PlantTribes},}
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131 </citation>
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132 </xml>
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133 <xml name="citations2to4">
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134 <citation type="bibtex">
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135 @article{Sasidharan2012,
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136 journal = {Nucleic Acids Research},
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137 author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
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138 title = {GFam: a platform for automatic annotation of gene families},
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139 year = {2012},
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140 pages = {gks631},}
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141 </citation>
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142 <citation type="bibtex">
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143 @article{Li2003,
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144 journal = {Genome Research}
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145 author = {3. Li L, Stoeckert CJ, Roos DS},
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146 title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
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147 year = {2003},
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148 volume = {13},
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149 number = {9},
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150 pages = {2178-2189},}
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151 </citation>
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152 <citation type="bibtex">
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153 @article{Emms2015,
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154 journal = {Genome Biology}
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155 author = {4. Emms DM, Kelly S},
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156 title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
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157 year = {2015},
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158 volume = {16},
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159 number = {1},
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160 pages = {157},}
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161 </citation>
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162 </xml>
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163 </macros>
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