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1 <tool id="plant_tribes_phylogenomics_analysis" name="Create multiple sequence alignments" version="0.3">
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2 <description>and inferred maximum likelihood phylogenies</description>
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3 <requirements>
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51
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4 <requirement type="package" version="0.3">plant_tribes_phylogenomics_analysis
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5 </requirement>
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6 </requirements>
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7 <stdio>
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8 <!-- Anything other than zero is an error -->
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 <!-- In case the return code has not been set propery check stderr too -->
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12 <regex match="Error:" />
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13 <regex match="Exception:" />
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14 </stdio>
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15 <command>
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16 <![CDATA[
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17 #import os
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18 #import sys
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19
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20 #set input_format = $input_format_cond.input_format
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21 #set pipeline_output_dir = 'phylogenomicsAnalysis_dir'
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22 #set scaffold_path = $scaffold.fields.path
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23 #set scaffold_dir = $os.path.split($scaffold_path)[0]
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24 #set scaffold_selection = $os.path.split($scaffold_path)[1]
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25 #set src_aln_dir = $os.path.join($pipeline_output_dir, 'orthogroups_aln')
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26 #set src_fasta_dir = $os.path.join($pipeline_output_dir, 'orthogroups_fasta')
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27 #set src_tree_dir = $os.path.join($pipeline_output_dir, 'orthogroups_tree')
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28
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29 #if str($input_format) == 'ptortho':
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30 #set dest_fasta_dir = $output_fasta_ptortho.extra_files_path
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31 #set multiple_codon_alignments = 'no'
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32 #set use_corresponding_coding_sequences = 'no'
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33 #else:
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34 #set dest_fasta_dir = $output_fasta_ptorthocs.extra_files_path
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35 #set multiple_codon_alignments_cond = $input_format_cond.multiple_codon_alignments_cond
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36 #set multiple_codon_alignments = $multiple_codon_alignments_cond.multiple_codon_alignments
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37 #if str($multiple_codon_alignments) == 'yes':
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38 #set use_corresponding_coding_sequences_cond = $multiple_codon_alignments_cond.use_corresponding_coding_sequences_cond
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39 #set use_corresponding_coding_sequences = $use_corresponding_coding_sequences_cond.use_corresponding_coding_sequences
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40 #else:
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41 #set use_corresponding_coding_sequences = 'no'
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42 #end if
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43 #end if
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42
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44 mkdir -p $dest_fasta_dir &&
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45
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46 #if str($options_type.options_type_selector) == 'advanced':
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47 #set multiple_sequence_alignments_cond = $options_type.multiple_sequence_alignments_cond
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48 #set multiple_sequence_alignments = $multiple_sequence_alignments_cond.multiple_sequence_alignments
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49 #if str($multiple_sequence_alignments) == 'yes':
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50 #set multiple_sequence_alignments_option_cond = $options_type.multiple_sequence_alignments_cond.multiple_sequence_alignments_option_cond
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51 #set multiple_sequence_alignments_option = $multiple_sequence_alignments_option_cond.multiple_sequence_alignments_option
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52 #set generate_output_aln = True
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53 #set dest_aln_dir = $output_aln.extra_files_path
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54 mkdir -p $dest_aln_dir &&
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55 #else:
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56 #set generate_output_aln = False
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57 #end if
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48
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58 #else:
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59 #set generate_output_aln = False
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46
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60 #end if
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61
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62 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
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63 #set generate_output_tree = True
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64 #set dest_tree_dir = $output_tree.extra_files_path
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65 mkdir -p $dest_tree_dir &&
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66 #else:
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67 #set generate_output_tree = False
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68 #end if
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69
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70 PhylogenomicsAnalysis
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71 --num_threads \${GALAXY_SLOTS:-4}
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72 #if str($input_format) == 'ptortho':
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73 --orthogroup_faa '$input_format_cond.input_ptortho.extra_files_path'
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74 #else:
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75 --orthogroup_faa '$input_format_cond.input_ptorthocs.extra_files_path'
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76 --orthogroup_fna
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77 #end if
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78 --scaffold_dir '$scaffold_dir'
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79 --scaffold '$scaffold_selection'
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80 --method $method
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81
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82 #if str($options_type.options_type_selector) == 'advanced':
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83 #if str($multiple_sequence_alignments) == 'yes':
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84 #if str($multiple_sequence_alignments_option) == 'create_alignments':
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85 --create_alignments
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5
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86 #else if str($multiple_sequence_alignments_option) == 'add_alignments':
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87 --add_alignments
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88 #else if str($multiple_sequence_alignments_option) == 'pasta_alignments':
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89 --pasta_script_path '$__tool_directory__/run_pasta.py'
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90 --pasta_alignments
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91 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
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92 #end if
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93 #end if
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94
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95 #if str($options_type.phylogenetic_trees_cond.phylogenetic_trees) == 'yes':
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96 #set tree_inference_cond = $options_type.phylogenetic_trees_cond.tree_inference_cond
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97 #set tree_inference_method = $tree_inference_cond.tree_inference
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98 --tree_inference $tree_inference_method
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99 #if str($tree_inference_method) == 'raxml':
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100 #set rooting_order_file_cond = $tree_inference_cond.rooting_order_file_cond
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101 #set rooting_order_file = $rooting_order_file_cond.rooting_order_file
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102 #if str($rooting_order_file) == 'yes':
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103 --rooting_order '$rooting_order_file_cond.rooting_order'
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104 #else:
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105 #set default_rooting_order = $__tool_directory__/rooting_order.config
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106 --rooting_order '$default_rooting_order'
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107 #end if
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108 --bootstrap_replicates $tree_inference_cond.bootstrap_replicates
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109 #end if
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110 --max_orthogroup_size $options_type.phylogenetic_trees_cond.max_orthogroup_size
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111 --min_orthogroup_size $options_type.phylogenetic_trees_cond.min_orthogroup_size
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112 #end if
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113
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114 #if str($options_type.msa_quality_control_options_cond.msa_quality_control_options) == 'yes':
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115 #set msa_quality_control_options_cond = $options_type.msa_quality_control_options_cond
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116 #set remove_gappy_sequences_cond = $msa_quality_control_options_cond.remove_gappy_sequences_cond
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117 #if str($remove_gappy_sequences_cond) == 'yes':
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118 #set trim_type_cond = $remove_gappy_sequences_cond.trim_type_cond
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119 --remove_sequences $remove_gappy_sequences_cond.remove_sequences
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120 #if str($trim_type_cond.trim_type) == 'automated_trimming':
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121 --automated_trimming
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122 #else:
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123 --gap_trimming $trim_type_cond.gap_trimming
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124 #end if
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125 #end if
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126 #end if
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127 #end if
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128 >/dev/null
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129
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130 && echo "Sequence alignments and corresponding phylogenies"
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131 #if str($input_format) == 'ptortho':
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132 && echo -e "#Size\tName" > $output_fasta_ptortho
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133 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptortho
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134 #else:
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135 && echo -e "#Size\tName" > $output_fasta_ptorthocs
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136 && ls -l $src_fasta_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_fasta_ptorthocs
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137 #end if
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138 && mv $src_fasta_dir/* $dest_fasta_dir || true
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139
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140 #if $generate_output_aln:
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141 && echo -e "#Size\tName" > $output_aln
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142 && ls -l $src_aln_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_aln
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143 && mv $src_aln_dir/* $dest_aln_dir || true
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144 #end if
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145
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146 #if $generate_output_tree:
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147 && echo -e "#Size\tName" > $output_tree
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148 && ls -l $src_tree_dir | grep f | awk -F ' ' '{print $5"\t"$9}' >> $output_tree
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149 && mv $src_tree_dir/* $dest_tree_dir || true
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150 #end if
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151 ]]>
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152 </command>
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153 <inputs>
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154 <conditional name="input_format_cond">
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155 <param name="input_format" type="select" label="Select type of data to sub sample">
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156 <option value="ptortho">Precomputed orthologous gene family clusters</option>
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157 <option value="ptorthocs">Precomputed orthologous gene family clusters with corresponding coding sequences</option>
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158 </param>
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159 <when value="ptortho">
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160 <param name="input_ptortho" format="ptortho" type="data" label="Precomputed orthologous gene family clusters" />
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161 </when>
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162 <when value="ptorthocs">
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163 <param name="input_ptorthocs" format="ptorthocs" type="data" label="Precomputed orthologous gene family clusters with corresponding coding sequences" />
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164 <conditional name="multiple_codon_alignments_cond">
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165 <param name="multiple_codon_alignments" type="select" label="Construct orthogroup multiple codon alignments?">
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166 <option value="no" selected="True">No</option>
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167 <option value="yes">Yes</option>
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168 </param>
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169 <when value="no" />
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170 <when value="yes">
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171 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference (dna)">
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172 <option value="protein" selected="true">Amino acid based</option>
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173 <option value="dna">Nucleotide based</option>
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174 </param>
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175 <conditional name="use_corresponding_coding_sequences_cond">
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176 <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences?">
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177 <option value="no" selected="true">No</option>
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178 <option value="yes">Yes</option>
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179 </param>
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180 <when value="no" />
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181 <when value="yes" />
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182 </conditional>
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183 </when>
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184 </conditional>
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185 </when>
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186 </conditional>
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187 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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188 <options from_data_table="plant_tribes_scaffolds" />
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189 <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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190 </param>
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191 <param name="method" type="select" label="Protein clustering method">
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192 <option value="gfam" selected="true">GFam</option>
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193 <option value="orthofinder">OrthoFinder</option>
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194 <option value="orthomcl">OrthoMCL</option>
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195 </param>
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196 <conditional name="options_type">
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197 <param name="options_type_selector" type="select" label="Options Configuration">
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198 <option value="basic" selected="true">Basic</option>
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199 <option value="advanced">Advanced</option>
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200 </param>
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201 <when value="basic" />
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202 <when value="advanced">
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203 <conditional name="multiple_sequence_alignments_cond">
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204 <param name="multiple_sequence_alignments" type="select" label="Set multiple sequence alignments options?">
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205 <option value="no" selected="true">No</option>
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206 <option value="yes">Yes</option>
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207 </param>
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208 <when value="no" />
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209 <when value="yes">
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210 <conditional name="multiple_sequence_alignments_option_cond">
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211 <param name="multiple_sequence_alignments_option" label="Select method for multiple sequence alignments" type="select"
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212 force_select="True">
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213 <option value="create_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (MAFFT algorithm)</option>
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214 <option value="add_alignments">Add unaligned orthogroup proteins to scaffold backbone multiple sequence alignments (MAFFT algorithm)</option>
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215 <option value="pasta_alignments">Create orthogroup protein multiple sequence alignments including scaffold backbone proteins (PASTA algorithm)</option>
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216 </param>
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217 <when value="create_alignments" />
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218 <when value="add_alignments" />
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219 <when value="pasta_alignments">
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220 <param name="pasta_iter_limit" type="integer" value="3" min="0" label="Maximum number of iteration that the PASTA algorithm will run" />
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221 </when>
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222 </conditional>
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223 </when>
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224 </conditional>
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225 <conditional name="phylogenetic_trees_cond">
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226 <param name="phylogenetic_trees" type="select" label="Set phylogenetic trees options?">
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227 <option value="no" selected="true">No</option>
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228 <option value="yes">Yes</option>
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229 </param>
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230 <when value="no" />
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231 <when value="yes">
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232 <conditional name="tree_inference_cond">
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233 <param name="tree_inference" type="select" label="Phylogenetic trees inference method">
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234 <option value="raxml" selected="true">RAxML</option>
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235 <option value="fasttree">FastTree</option>
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236 </param>
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237 <when value="raxml">
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238 <conditional name="rooting_order_file_cond">
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239 <param name="rooting_order_file" type="select" label="Select rooting order configuration for rooting trees?" help="Select no for the default rooting order configuration which uses the most distant taxon present in the orthogroup">
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240 <option value="no" selected="true">No</option>
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241 <option value="yes">Yes</option>
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242 </param>
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243 <when value="no" />
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244 <when value="yes">
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245 <param name="rooting_order" format="txt" type="data" label="Rooting order configuration for rooting trees" />
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246 </when>
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247 </conditional>
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248 <param name="bootstrap_replicates" type="integer" value="100" min="0" label="Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree" />
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249 </when>
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250 <when value="fasttree" />
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251 </conditional>
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252 <param name="max_orthogroup_size" type="integer" value="100" min="0" label="Maximum number of sequences in orthogroup alignments" />
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253 <param name="min_orthogroup_size" type="integer" value="4" min="0" label="Minimum number of sequences in orthogroup alignments" />
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254 </when>
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255 </conditional>
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256 <conditional name="msa_quality_control_options_cond">
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257 <param name="msa_quality_control_options" type="select" label="Set MSA quality control options?">
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258 <option value="no" selected="true">No</option>
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259 <option value="yes">Yes</option>
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260 </param>
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261 <when value="no" />
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262 <when value="yes">
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263 <conditional name="remove_gappy_sequences_cond">
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264 <param name="remove_gappy_sequences" type="select" label="Remove gappy sequences in alignments?">
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265 <option value="no" selected="true">No</option>
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266 <option value="yes">Yes</option>
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267 </param>
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268 <when value="no" />
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269 <when value="yes">
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270 <param name="remove_sequences" type="float" value="0.5" min="0" max="1" label="Remove sequences with gaps of" help="0.5 removes sequences with 50% gaps" />
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271 <conditional name="trim_type_cond">
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272 <param name="trim_type" type="select" label="Select process used for gap trimming">
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273 <option value="gap_trimming" selected="true">Nucleotide based </option>
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274 <option value="automated_trimming">Trim alignments using trimAl's ML heuristic trimming approach</option>
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0
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275 </param>
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276 <when value="automated_trimming" />
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277 <when value="gap_trimming">
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278 <param name="gap_trimming" type="float" value="0.1" min="0" max="1.0" label="Remove sites in alignments with gaps of" help="0.1 removes sites with 90% gaps" />
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0
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279 </when>
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280 </conditional>
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281 </when>
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282 </conditional>
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283 </when>
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284 </conditional>
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285 </when>
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286 </conditional>
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287 </inputs>
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288 <outputs>
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289 <data name="output_fasta_ptortho" format="ptortho">
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290 <filter>input_format_cond['input_format'] == 'ptortho'</filter>
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291 </data>
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51
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292 <data name="output_fasta_ptorthocs" format="ptorthocs">
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293 <filter>input_format_cond['input_format'] == 'ptorthocs'</filter>
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41
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294 </data>
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54
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295 <data name="output_aln" format="ptalign" label="Multiple alignments using method ${options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments_option_cond']['multiple_sequence_alignments_option']} on ${on_string}">
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22
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296 <filter>options_type['options_type_selector'] == 'advanced' and options_type['multiple_sequence_alignments_cond']['multiple_sequence_alignments'] == 'yes'</filter>
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297 </data>
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298 <data name="output_tree" format="pttree" label="Phylogenetic trees on ${on_string}">
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299 <filter>options_type['options_type_selector'] == 'advanced' and options_type['phylogenetic_trees_cond']['phylogenetic_trees'] == 'yes'</filter>
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300 </data>
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0
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301 </outputs>
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302 <tests>
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303 <test>
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304 </test>
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305 </tests>
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306 <help>
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307 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
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308 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. It performs phylogenomic
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309 analyses by creating multiple sequence alignments and inferred maximum likelihood phylogenies for orthogroups produced by the
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310 **Classify gene sequences into precomputed orthologous gene family clusters** tool.
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311
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312 -----
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313
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314 **Options**
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315
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51
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316 * **Required options**
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18
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317
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318 - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences.
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319 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
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320 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
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321 * **Multiple sequence alignments options**
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14
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322
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323 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
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324 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'.
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325 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
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326 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
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327 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error.
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328
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329 * **Phylogenetic trees options**
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15
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330
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331 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
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56
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332 - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
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333 - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
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334 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
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335 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
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14
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336
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337 * **MSA quality control options**
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14
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338
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51
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339 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
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340 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.
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341 - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
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14
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342
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343 </help>
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344 <citations>
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51
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345 <citation type="bibtex">
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346 @unpublished{None,
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347 author = {Eric Wafula},
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348 title = {None},
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349 year = {None},
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350 url = {https://github.com/dePamphilis/PlantTribes}
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351 }
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352 </citation>
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353 <citation type="doi">10.1093/bioinformatics/btw412</citation>
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354 <citation type="bibtex">
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355 @published{Research in Computational Molecular Biology (RECOMB) (pp. 177–191),
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356 author = {Mirarab, S., Nguyen, N., Warnow, T.},
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357 title = {PASTA: Ultra-Large Multiple Sequence Alignment. In R. Sharan
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358 (Ed.)},
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359 year = {2014},
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360 url = {https://github.com/smirarab/pasta}
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361 }
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362 </citation>
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363 <citation type="bibtex">
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364 @published{Bioinformatics,
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365 author = {Salvador Capella-Gutierrez, Jose M. Silla-Martinez, Toni
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366 Gabaldon},
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367 title = {trimAl: a tool for automated alignment trimming in large-scale
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368 phylogenetic analyses},
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369 year = {2009},
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370 url = {http://trimal.cgenomics.org}
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371 }
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372 </citation>
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373 <citation type="bibtex">
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374 @published{Bioinformatics,
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375 author = {A. Stamatakis},
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376 title = {RAxML Version 8: A tool for Phylogenetic Analysis and
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377 Post-Analysis of Large Phylogenies},
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378 year = {2014},
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379 url = {http://sco.h-its.org/exelixis/web/software/raxml/index.html}
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380 }
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381 </citation>
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382 <citation type="doi">10.1371/journal.pone.0009490</citation>
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0
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383 </citations>
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384 </tool>
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