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