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1 <tool id="plant_tribes_kaks_analysis" name="Perform orthologous or paralogous ks analyses" version="0.8.0">
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2 <description>of coding sequences and amino acid sequences</description>
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3 <requirements>
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4 <requirement type="package" version="0.8">plant_tribes_kaks_analysis</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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16 #set output_dir = 'kaksAnalysis_dir'
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17 #set comparison = $comparison_cond.comparison
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18 #if str($options_type.options_type_selector) == 'advanced':
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19 #set codeml_ctl_file_cond = $options_type.codeml_ctl_file_cond
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20 #set codeml_ctl_file_select = $codeml_ctl_file_cond.codeml_ctl_file_select
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21 #set fit_components_cond = $options_type.fit_components_cond
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22 #set fit_components = $fit_components_cond.fit_components
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23 #set recalibrate_cond = $options_type.recalibrate_cond
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24 #set recalibrate = $recalibrate_cond.recalibrate
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25 #set set_min_coverage_cond = $options_type.set_min_coverage_cond
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26 #set set_min_coverage = $set_min_coverage_cond.set_min_coverage
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17
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27 #set set_lower_ks_limit_cond = $options_type.set_lower_ks_limit_cond
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16
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28 #set set_lower_ks_limit = $set_lower_ks_limit_cond.set_lower_ks_limit
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17
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29 #set set_upper_ks_limit_cond = $options_type.set_upper_ks_limit_cond
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30 #set set_upper_ks_limit = $set_upper_ks_limit_cond.set_upper_ks_limit
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31 #else:
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32 #set codeml_ctl_file_select = 'no'
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33 #set fit_components = 'no'
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34 #set set_lower_ks_limit = 'no'
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35 #set set_upper_ks_limit = 'no'
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36 #end if
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37 KaKsAnalysis
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38 --config_dir '$scaffold.fields.path'
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39 --num_threads \${GALAXY_SLOTS:-4}
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40 --coding_sequences_species_1 '$coding_sequences_species_1'
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41 --proteins_species_1 '$proteins_species_1'
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42 --comparison $comparison
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43 #if str($comparison) == 'orthologs':
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44 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
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45 --proteins_species_2 '$comparison_cond.proteins_species_2'
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46 #end if
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47 #if str($options_type.options_type_selector) == 'advanced':
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48 #if str($set_min_coverage) == 'yes':
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49 --min_coverage $set_min_coverage_cond.min_coverage
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50 #end if
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51 #if str($recalibrate) == 'yes':
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52 --recalibration_rate $recalibrate_cond.recalibration_rate
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53 #end if
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54 #if str($codeml_ctl_file_select) == 'yes':
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55 --codeml_ctl_file '$codeml_ctl_file_cond.codeml_ctl_file'
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56 # No else block needed here because the default codeml_ctl config
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57 # will be used if the --codeml_ctl_file flag is missing.
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58 #end if
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59 #if str($fit_components) == 'yes':
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60 --fit_components
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61 --num_of_components $fit_components_cond.num_of_components
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62 #end if
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63 #if str($set_lower_ks_limit) == 'yes':
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64 --min_ks $set_lower_ks_limit_cond.min_ks
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65 #end if
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66 #if str($set_upper_ks_limit) == 'yes':
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67 --max_ks $set_upper_ks_limit_cond.max_ks
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68 #end if
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69 #end if
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70 >/dev/null
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71 && mv $output_dir/species1.fna '$output_species1_fna'
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72 && mv $output_dir/species1.faa '$output_species1_faa'
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73 #if str($comparison) == 'paralogs':
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74 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
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9
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75 #else:
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76 && mv $output_dir/species2.faa '$output_species2_faa'
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77 && mv $output_dir/species2.fna '$output_species2_fna'
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78 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
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79 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
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80 #end if
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81 && mv $output_dir/*.rbhb '$output_rbhb'
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82 && mv $output_dir/*.kaks '$output_kaks'
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83 #if str($fit_components) == 'yes':
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84 && mv $output_dir/*.components '$output_components'
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85 #end if
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86 ]]>
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87 </command>
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88 <inputs>
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89 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for species1" />
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90 <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for species1" />
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91 <conditional name="comparison_cond">
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92 <param name="comparison" type="select" label="Select method for pairwise sequence comparison to determine homolgous pairs" help="Cross species comparison requires selection of inputs for second species">
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93 <option value="paralogs" selected="true">Self species comparison</option>
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94 <option value="orthologs">Cross species comparison</option>
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95 </param>
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96 <when value="paralogs" />
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97 <when value="orthologs">
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98 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for species2" />
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99 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for species2" />
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0
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100 </when>
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101 </conditional>
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102 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold" help="Selection specifies default configuration files">
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103 <options from_data_table="plant_tribes_scaffolds" />
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104 <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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105 </param>
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106 <conditional name="options_type">
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107 <param name="options_type_selector" type="select" label="Options Configuration">
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108 <option value="basic" selected="true">Basic</option>
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109 <option value="advanced">Advanced</option>
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110 </param>
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111 <when value="basic" />
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112 <when value="advanced">
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113 <conditional name="set_min_coverage_cond">
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114 <param name="set_min_coverage" type="select" label="Specify minimum sequence pairwise coverage length between homologous pairs?">
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115 <option value="no" selected="true">No</option>
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116 <option value="yes">Yes</option>
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117 </param>
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118 <when value="no" />
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119 <when value="yes">
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120 <param name="min_coverage" type="float" value="0.5" min="0.3" max="1.0" label="Minimum sequence pairwise coverage length between homologous pairs" />
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121 </when>
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122 </conditional>
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123 <conditional name="recalibrate_cond">
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124 <param name="recalibrate" type="select" label="Specify evolutionary rate for recalibrating synonymous subsitutions (ks) of species?">
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125 <option value="no" selected="true">No</option>
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126 <option value="yes">Yes</option>
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127 </param>
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128 <when value="no" />
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129 <when value="yes">
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130 <param name="recalibration_rate" type="float" value="0.0" min="0.0" label="Evolutionary rate for recalibrating synonymous subsitutions (ks) of species" />
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131 </when>
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132 </conditional>
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133 <conditional name="codeml_ctl_file_cond">
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134 <param name="codeml_ctl_file_select" type="select" label="Select PAML codeml control file?" help="Used for ML analysis of protein-coding DNA sequences using codon substitution models, select No to use the default control file">
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135 <option value="no" selected="true">No</option>
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136 <option value="yes">Yes</option>
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137 </param>
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138 <when value="no" />
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139 <when value="yes">
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140 <param name="codeml_ctl_file" format="txt" type="data" label="PAML codeml control file" />
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141 </when>
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142 </conditional>
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143 <conditional name="fit_components_cond">
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144 <param name="fit_components" type="select" label="Fit a mixture model of multivariate normal components to synonymous (ks) distribution?" help="Used to identify significant duplication events in a genome">
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145 <option value="no" selected="true">No</option>
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146 <option value="yes">Yes</option>
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147 </param>
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148 <when value="no" />
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149 <when value="yes">
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150 <param name="num_of_components" type="integer" value="0" min="0" label="Number components to fit to synonymous subsitutions (ks) distribution" />
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151 </when>
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152 </conditional>
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153 <conditional name="set_lower_ks_limit_cond">
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154 <param name="set_lower_ks_limit" type="select" label="Set lower limit of synonymous subsitutions (ks)?" help="Reduces background noise from young paralogous pairs due to normal gene births and deaths in a genome">
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155 <option value="no" selected="true">No</option>
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156 <option value="yes">Yes</option>
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157 </param>
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158 <when value="no" />
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159 <when value="yes">
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160 <param name="min_ks" type="float" value="0.0" min="0.0" label="Lower limit of synonymous subsitutions (ks)" />
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161 </when>
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162 </conditional>
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163 <conditional name="set_upper_ks_limit_cond">
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164 <param name="set_upper_ks_limit" type="select" label="Set upper limit of synonymous subsitutions (ks)?" help="Excludes likey ancient paralogous pairs">
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165 <option value="no" selected="true">No</option>
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166 <option value="yes">Yes</option>
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167 </param>
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168 <when value="no" />
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169 <when value="yes">
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170 <param name="max_ks" type="float" value="0.0" min="0.0" label="Upper limit of synonymous subsitutions (ks)" />
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0
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171 </when>
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172 </conditional>
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173 </when>
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174 </conditional>
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175 <!-- Required due to the Emmix license -->
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176 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
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177 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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178 </param>
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179 </inputs>
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180 <outputs>
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181 <data name="output_species1_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}" />
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182 <data name="output_species1_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}" />
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183 <data name="output_species2_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}">
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184 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
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185 </data>
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186 <data name="output_species2_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}">
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187 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
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188 </data>
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189 <data name="output_species1_paralog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
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190 <filter>comparison_cond['comparison'] == 'paralogs'</filter>
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191 </data>
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192 <data name="output_species1_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
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193 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
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194 </data>
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195 <data name="output_species2_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
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196 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
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197 </data>
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198 <data name="output_rbhb" format="tabular" label="KaKs analysis (paralogous pairs) on ${on_string}" />
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199 <data name="output_kaks" format="tabular" label="KaKs analysis on ${on_string}" />
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200 <data name="output_components" format="tabular" label="KaKs analysis (significant components in the ks distribution) on ${on_string}">
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201 <filter>options_type['options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes'</filter>
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202 </data>
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203 </outputs>
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204 <tests>
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205 <test>
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206 </test>
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207 </tests>
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208 <help>
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209 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
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210 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. This tool performs orthologous
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211 or paralogous ks analyses of coding sequences and amino acid sequences.
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212
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213 -----
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214
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215 **Options**
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216
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217 * **Required**
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218
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219 - **Coding sequences (CDS) fasta file for species1** - Coding sequences (CDS) fasta file for species1.
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220 - **Aamino acids (proteins) sequences fasta file for species1** - Aamino acids (proteins) sequences fasta file for species1
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221 - **Select method for pairwise sequence comparison to determine homolgous pairs** - Pairwise sequence comparison to determine homolgous pairs (cross species comparison requires selection of inputs for species2).
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222 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool.
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223
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224 * **Optional**
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225
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226 - **Minimum sequence pairwise coverage length between homologous pairs** - Minimum sequence pairwise coverage length between homologous pairs (e.g., 0.5 results in 50% coverage. Legal values lie between 0.3 and 1.0.
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227 - **Evolutionary rate for recalibrating synonymous subsitutions (ks) of species** - (applies to paralogous ks analysis) Recalibrate synonymous subsitutions (ks) of species using a predetermined evoutionary rate that can be determined from a species tree inferred from a collection single copy genes from taxa of interest (Cui et al., 2006).
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228 - **Select PAML codeml control file?** - Select PAML's codeml control file from your history. This file is used to to perfom ML analysis of protein-coding DNA sequences using codon substitution models. Selecting No uses the default file which does not include input (seqfile, treefile) and output (outfile) parameters of codeml.
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229 - **Fit a mixture model of multivariate normal components to synonymous (ks) distribution?** - Fit a mixture model of multivariate normal components to synonymous (ks) distribution to identify significant duplication event(s) in a genome.
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230 - **Number components to fit to synonymous subsitutions (ks) distribution** - Number components to fit to synonymous subsitutions (ks) distribution.
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231 - **Lower limit of synonymous subsitutions (ks)** - Lower limit of synonymous subsitutions (ks) - necessary if fitting components to the distribution to reduce background noise from young paralogous pairs due to normal gene births and deaths in a genome.
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232 - **Upper limit of synonymous subsitutions (ks)** - Upper limit of synonymous subsitutions (ks) - necessary if fitting components to the distribution to exclude likey ancient paralogous pairs.
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233
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234 </help>
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235 <citations>
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236 <citation type="bibtex">
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237 @unpublished{None,
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238 author = {Eric Wafula},
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239 title = {None},
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240 year = {None},
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241 url = {https://github.com/dePamphilis/PlantTribes}
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242 }
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243 </citation>
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244 <citation type="doi">10.1093/bioinformatics/btw412</citation>
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245 <citation type="doi">10.1186/1471-2105-10-421</citation>
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246 <citation type="doi">10.1093/molbev/msm088</citation>
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247 <citation type="doi">10.18637/jss.v004.i02</citation>
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248 </citations>
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249 </tool>
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