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28
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1 <tool id="plant_tribes_gene_family_classifier" name="Classify gene sequences" version="0.3">
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2 <description>into precomputed orthologous gene family clusters</description>
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0
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3 <requirements>
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28
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4 <requirement type="package" version="0.3">plant_tribes_gene_family_classifier</requirement>
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0
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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29
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9 <exit_code range=":-1" />
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10 <!-- In case the return code has not been set propery check stderr too -->
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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39
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16 #import os
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17 #set scaffold_path = $scaffold.fields.path
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18 #set scaffold_dir = $os.path.split($scaffold_path)[0]
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19 #set scaffold_selection = $os.path.split($scaffold_path)[1]
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35
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20
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21
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21 #if str($options_type.options_type_selector) == 'advanced':
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51
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22 #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
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23 #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
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17
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24 #set create_orthogroup_cond = $options_type.create_orthogroup_cond
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25 #set create_orthogroup = $create_orthogroup_cond.create_orthogroup
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44
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26 #set specify_single_copy_cond = $options_type.specify_single_copy_cond
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46
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27 #set specify_single_copy = $specify_single_copy_cond.specify_single_copy
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44
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28
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51
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29 #if str($specify_super_orthogroups) == 'yes':
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30 #set specify_super_orthos = True
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31 #set super_orthogroups = $specify_super_orthogroups_cond.super_orthogroups
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32 #else:
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33 #set specify_super_orthos = False
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34 #end if
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35
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21
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36 #if str($create_orthogroup) == 'yes':
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44
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37 #set create_ortho_sequences = True
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38 #set orthogroups_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
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21
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39 #set create_corresponding_coding_sequences_cond = $create_orthogroup_cond.create_corresponding_coding_sequences_cond
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44
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40
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21
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41 #if str($create_corresponding_coding_sequences_cond.create_corresponding_coding_sequences) == 'yes':
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42 #set create_corresponding_coding_sequences = True
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45
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43 #set orthogroups_fasta_dest_dir = $output_ptcgfcs.extra_files_path
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21
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44 #else:
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45 #set create_corresponding_coding_sequences = False
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44
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46 #set orthogroups_fasta_dest_dir = $output_ptcgf.extra_files_path
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47 #end if
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48 mkdir -p $orthogroups_fasta_dest_dir &&
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21
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49 #else:
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50 #set create_ortho_sequences = False
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23
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51 #set create_corresponding_coding_sequences = False
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21
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52 #end if
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52
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53
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54 #if str($specify_single_copy) == 'yes':
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55 #set single_copy_orthogroup = True
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56 #set single_copy_cond = $specify_single_copy_cond.single_copy_cond
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57 ## FixMe: the single_copy_custom option is not currently supported.
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58 #set single_copy = $single_copy_cond.single_copy
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59 #if $create_ortho_sequences:
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60 #set single_copy_fasta_src_dir = $os.path.join('geneFamilyClassification_dir', 'single_copy_fasta')
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61 #set single_copy_fasta_dest_dir = $output_ptsco.extra_files_path
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62 mkdir -p $single_copy_fasta_dest_dir &&
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63 #end if:
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64 #else:
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65 #set single_copy_orthogroup = False
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66 #end if
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67
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13
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68 #else:
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69 #set single_copy_orthogroup = False
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70 #set create_ortho_sequences = False
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71 #set create_corresponding_coding_sequences = False
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4
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72 #end if
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73
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74 GeneFamilyClassifier
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75 --proteins '$input'
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76 --scaffold_dir '$scaffold_dir'
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77 --scaffold '$scaffold_selection'
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78 --method $method
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79 --classifier $save_hmmscan_log_cond.classifier
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80 --num_threads \${GALAXY_SLOTS:-4}
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81
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0
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82 #if str($options_type.options_type_selector) == 'advanced':
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51
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83 #if specify_super_orthos:
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84 --super_orthogroups $super_orthogroups
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85 #end if
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47
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86 #if $single_copy_orthogroup:
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44
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87 --single_copy_taxa $single_copy_cond.single_copy_taxa
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88 --taxa_present $single_copy_cond.taxa_present
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89 #end if
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90 #if str($create_orthogroup) == 'yes':
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91 --orthogroup_fasta
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92 #if $create_corresponding_coding_sequences:
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93 --coding_sequences '$create_corresponding_coding_sequences_cond.coding_sequences'
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17
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94 #end if
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0
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95 #end if
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96 #end if
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44
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97 >/dev/null
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98
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99 #if str($save_hmmscan_log_cond.classifier) == 'hmmscan' or str($save_hmmscan_log_cond.classifier) == 'both':
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100 #if str($save_hmmscan_log_cond.save_hmmscan_log) == 'yes':
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101 && mv geneFamilyClassification_dir/hmmscan.log $hmmscan_log
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13
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102 #else:
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103 && rm geneFamilyClassification_dir/hmmscan.log
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13
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104 #end if
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12
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105 #end if
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106
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107 #if $create_ortho_sequences and $os.path.exists($orthogroups_fasta_src_dir) and len($os.listdir($orthogroups_fasta_src_dir)) > 0:
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108 #if $create_corresponding_coding_sequences:
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109 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgfcs
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110 #else:
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111 && ls -l $orthogroups_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptcgf
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112 #end if
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113 && mv $orthogroups_fasta_src_dir/* $orthogroups_fasta_dest_dir
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4
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114 #end if
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115
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47
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116 #if $single_copy_orthogroup:
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52
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117 #if $create_ortho_sequences and $os.path.exists($single_copy_fasta_src_dir) and len($os.listdir($single_copy_fasta_src_dir)) > 0:
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118 && ls -l $single_copy_fasta_src_dir | grep f | awk -F ' ' '{print $5"\t"$9}' > $output_ptsco
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50
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119 && mv $single_copy_fasta_src_dir/* $single_copy_fasta_dest_dir
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120 #else:
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121 && mv geneFamilyClassification_dir/*.singleCopy $output_single_copy
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48
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122 #end if
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44
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123 #end if
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0
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124 ]]>
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125 </command>
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126 <inputs>
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127 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/>
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128 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
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129 <options from_data_table="plant_tribes_scaffolds" />
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39
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130 <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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0
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131 </param>
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132 <param name="method" type="select" label="Protein clustering method">
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133 <option value="gfam" selected="true">GFam</option>
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134 <option value="orthofinder">OrthoFinder</option>
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135 <option value="orthomcl">OrthoMCL</option>
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136 </param>
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13
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137 <conditional name="save_hmmscan_log_cond">
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138 <param name="classifier" type="select" label="Protein classification method">
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139 <option value="blastp" selected="true">blastp</option>
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140 <option value="hmmscan">HMMScan</option>
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141 <option value="both">Both blastp and HMMScan</option>
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142 </param>
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143 <when value="blastp" />
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144 <when value="hmmscan">
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145 <param name="save_hmmscan_log" type="select" label="Save hmmscan log?" help="Save the hmmscan log in an additional output dataset">
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146 <option value="no" selected="true">No</option>
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147 <option value="yes">Yes</option>
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148 </param>
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149 </when>
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150 <when value="both">
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151 <param name="save_hmmscan_log" type="select" label="Save hmmscan log?" help="Save the hmmscan log in an additional output dataset">
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152 <option value="no" selected="true">No</option>
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153 <option value="yes">Yes</option>
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154 </param>
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155 </when>
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156 </conditional>
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157 <conditional name="options_type">
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158 <param name="options_type_selector" type="select" label="Options Configuration">
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159 <option value="basic" selected="true">Basic</option>
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160 <option value="advanced">Advanced</option>
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161 </param>
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162 <when value="basic" />
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163 <when value="advanced">
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51
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164 <conditional name="specify_super_orthogroups_cond">
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165 <param name="specify_super_orthogroups" type="select" label="Specify super orthogroups?" help="Secondary MCL clusters of orthogroups">
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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="super_orthogroups" type="select" label="Super Orthogroups">
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172 <option value="min_evalue" selected="true">Minimum e-value</option>
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173 <option value="avg_evalue">Average e-value</option>
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174 </param>
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175 </when>
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176 </conditional>
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177 <conditional name="specify_single_copy_cond">
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178 <param name="specify_single_copy" type="select" label="Specify single copy orthogroup selection?">
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179 <option value="no" selected="true">No</option>
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180 <option value="yes">Yes</option>
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181 </param>
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182 <when value="no"/>
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183 <when value="yes">
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184 <conditional name="single_copy_cond">
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185 <param name="single_copy" type="select" label="Select single copy configuration">
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186 <!--
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187 FixMe: single_copy_custom is not currently supported because the
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188 ~/config/*.singleCopy.config files are not easy to manage by a suer
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189 and the GeneFamilyClassifier pipeline must be enhanced to provide an
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190 optional parameter for the hard-coded path to the config.
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191 <option value="custom" selected="true">Single copy orthogroup custom</option>
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192 -->
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193 <option value="taxa">Minumum single copy taxa required in orthogroup</option>
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194 </param>
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195 <when value="custom" />
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196 <when value="taxa">
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197 <param name="single_copy_taxa" type="integer" value="20" label="Minumum single copy taxa required in orthogroup"/>
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198 <param name="taxa_present" type="integer" value="21" label="Minumum taxa required in single copy orthogroup"/>
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199 </when>
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200 </conditional>
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201 </when>
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202 </conditional>
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203 <conditional name="create_orthogroup_cond">
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204 <param name="create_orthogroup" type="select" label="Create orthogroup fasta files?">
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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="create_corresponding_coding_sequences_cond">
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211 <param name="create_corresponding_coding_sequences" type="select" label="Create corresponding coding sequences?">
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212 <option value="no" selected="true">No</option>
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213 <option value="yes">Yes</option>
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214 </param>
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215 <when value="no" />
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216 <when value="yes">
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217 <param name="coding_sequences" format="fasta" type="data" label="Corresponding coding sequences (CDS) fasta file"/>
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218 </when>
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219 </conditional>
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220 </when>
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221 </conditional>
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222 </when>
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223 </conditional>
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224 </inputs>
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225 <outputs>
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226 <data name="hmmscan_log" format="txt" label="Protein classification hmmscan.log on ${on_string}">
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227 <filter>save_hmmscan_log_cond['classifier'] in ['hmmscan', 'both'] and save_hmmscan_log_cond['save_hmmscan_log'] == 'yes'</filter>
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228 </data>
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229 <data name="output_ptcgf" format="ptcgf" label="Gene family clusters on ${on_string}">
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230 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'no'</filter>
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31
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231 </data>
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232 <data name="output_ptcgfcs" format="ptcgfcs" label="Gene family clusters and corresponding coding sequences on ${on_string}">
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233 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['create_orthogroup_cond']['create_corresponding_coding_sequences_cond']['create_corresponding_coding_sequences'] == 'yes'</filter>
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234 </data>
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235 <data name="output_ptsco" format="txt" label="Single copy orthogroups on ${on_string}">
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53
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236 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'yes' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
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52
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237 </data>
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54
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238 <data name="output_single_copy" format="tabular" label="Single copy orthogroups on ${on_string}">
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53
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239 <filter>options_type['options_type_selector'] == 'advanced' and options_type['create_orthogroup_cond']['create_orthogroup'] == 'no' and options_type['specify_single_copy_cond']['specify_single_copy'] == 'yes'</filter>
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44
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240 </data>
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241 <collection name="orthos" type="list">
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242 <discover_datasets pattern="__name__" directory="geneFamilyClassification_dir" visible="false" ext="tabular" />
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0
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243 </collection>
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244 </outputs>
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245 <tests>
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246 <!-- Not sure how to test this since the tool requires scaffolds data which is extremely large and installed using a Data Manager -->
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247 <!--
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248 <test>
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249 <param name="input" value="transcripts.cleaned.nr.pep" ftype="fasta" />
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250 <param name="scaffold" value="22Gv1.1"/>
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251 <param name="method" value="orthomcl"/>
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252 <param name="classifier" value="blastp"/>
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253 <param name="dereplicate" value="yes"/>
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254 <param name="min_length" value="200"/>
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255 <output_collection name="orthos" type="list">
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256 <element name="proteins.blastp.22Gv1.1" file="proteins.blastp.22Gv1.1" ftype="tabular"/>
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257 <element name="proteins.blastp.22Gv1.1.bestOrthos" file="proteins.blastp.22Gv1.1.bestOrthos" ftype="tabular"/>
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258 <element name="proteins.blastp.22Gv1.1.bestOrthos.summary" file="proteins.blastp.22Gv1.1.bestOrthos.summary" ftype="tabular"/>
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0
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259 </output_collection>
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260 </test>
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261 -->
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262 </tests>
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263 <help>
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264 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
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265 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. This tool classifies gene
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266 sequences into precomputed orthologous gene family clusters using either blastp (faster), HMMScan (slower but more sensitive
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267 to remote homologs) or both (more exhaustive).
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268
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269 This tool accepts any of the following as input:
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28
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270
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271 * the postprocessed assemblies produced by the **Postprocess de novo assembly transcripts into putative coding sequences** tool
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272 * externally predicted coding sequences and their corresponding amino acid translations derived from a transcriptome assembly
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273 * gene predictions from a sequenced genome
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0
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274
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275 -----
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276
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277 **Options**
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278
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279 * **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
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280 * **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
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281 * **Protein classification method** - blastp (faster), HMMScan (slower but more sensative to the remote homologs) or both (more exhaustive).
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282 * **Super Orthogroups** - Secondary MCL clusters of orthogroups.
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45
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283 * **Specify single copy orthogroup selection?** - Select 'Yes' to specify one of 'Single copy orthogroup custom' (not yet supported) or 'Minumum single copy taxa required in orthogroup'.
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284 * **Minumum single copy taxa required in orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
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285 * **Minumum taxa required in single copy orthogroup** - Used with "Minumum single copy taxa required in orthogroup" configuration only.
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286 * **Corresponding coding sequences (CDS) fasta file** - Used only when selecting "Create orthogroup fasta files?".
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287
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288 </help>
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289 <citations>
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290 <citation type="bibtex">
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291 @unpublished{None,
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292 author = {Eric Wafula},
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0
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293 title = {None},
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294 year = {None},
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295 url = {https://github.com/dePamphilis/PlantTribes}
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296 }</citation>
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297 <citation type="doi">10.1186/1471-2105-10-421</citation>
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298 <citation type="bibtex">
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299 @unpublished{None,
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300 author = {None},
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301 title = {HMMER 3.1+ hmmscan search sequence(s) against a profile database},
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302 year = {2013},
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303 url = {http://hmmer.org/}
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0
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304 }</citation>
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305 </citations>
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306 </tool>
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