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