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1 <tool id="plant_tribes_kaks_analysis" name="Perform orthologous or paralogous ks analyses" version="0.7.0">
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2 <description>of coding sequences and amino acid sequences</description>
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0
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3 <requirements>
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4 <requirement type="package" version="0.7">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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5
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16 #set output_dir = 'kaksAnalysis_dir'
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4
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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 = $fit_components_cond.fit_components
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6
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23 #else:
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24 #set codeml_ctl_file_select = 'no'
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25 #set fit_components = 'no'
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0
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26 #end if
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27 KaKsAnalysis
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28 --config_dir '$scaffold.fields.path'
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29 --num_threads \${GALAXY_SLOTS:-4}
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30 --coding_sequences_species_1 '$coding_sequences_species_1'
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31 --proteins_species_1 '$proteins_species_1'
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32 --comparison $comparison
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4
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33 #if str($comparison) == 'orthologs':
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34 --coding_sequences_species_2 '$comparison_cond.coding_sequences_species_2'
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35 --proteins_species_2 '$comparison_cond.proteins_species_2'
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36 #end if
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37 #if str($options_type.options_type_selector) == 'advanced':
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38 --min_coverage $min_coverage
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39 --recalibration_rate $recalibration_rate
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40 #if str($codeml_ctl_file_select) == 'yes':
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41 --codeml_ctl_file '$codeml_ctl_file_cond.codeml_ctl_file'
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42 # No else block needed here because the default codeml_ctl config
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43 # will be used if the --codeml_ctl_file flag is missing.
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44 #end if
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45 #if str($fit_components) == 'yes':
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46 --num_of_components $fit_components_cond.num_of_components
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47 --min_ks $fit_components_cond.min_ks
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48 --max_ks $fit_components_cond.max_ks
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49 #end if
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50 #end if
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51 >/dev/null
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52 && mv $output_dir/species1.fna '$output_species1_fna'
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53 && mv $output_dir/species1.faa '$output_species1_faa'
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54 #if str($comparison) == 'orthologs':
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55 && mv $output_dir/species1.fna.blastn.paralogs '$output_species1_paralog'
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56 #end if
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57 #if str($comparison) == 'orthologs':
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58 && mv $output_dir/species2.faa '$output_species2_faa'
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59 && mv $output_dir/species2.fna '$output_species2_fna'
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60 && mv $output_dir/species1.fna.blastn.orthologs '$output_species1_ortholog'
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61 && mv $output_dir/species2.fna.blastn.orthologs '$output_species2_ortholog'
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62 #end if
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63 && mv $output_dir/*.rbhb '$output_rbhb'
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64 && mv $output_dir/*.kaks '$output_kaks'
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65 #if str($fit_components) == 'yes':
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66 && mv $output_dir/*.components '$output_components'
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67 #end if
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0
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68 ]]>
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69 </command>
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70 <inputs>
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71 <param name="coding_sequences_species_1" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the species" />
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3
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72 <param name="proteins_species_1" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the species" />
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0
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73 <conditional name="comparison_cond">
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74 <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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75 <option value="paralogs" selected="true">Self species comparison</option>
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76 <option value="orthologs">Cross species comparison</option>
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77 </param>
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78 <when value="paralogs" />
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79 <when value="orthologs">
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80 <param name="coding_sequences_species_2" format="fasta" type="data" label="Coding sequences (CDS) fasta file for the second species" />
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81 <param name="proteins_species_2" format="fasta" type="data" label="Aamino acids (proteins) sequences fasta file for the second species" />
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0
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82 </when>
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83 </conditional>
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84 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold" help="Selection specifies default configuration files">
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85 <options from_data_table="plant_tribes_scaffolds" />
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86 <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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87 </param>
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0
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88 <conditional name="options_type">
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89 <param name="options_type_selector" type="select" label="Options Configuration">
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90 <option value="basic" selected="true">Basic</option>
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91 <option value="advanced">Advanced</option>
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92 </param>
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93 <when value="basic" />
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94 <when value="advanced">
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95 <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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96 <param name="recalibration_rate" type="float" value="0.0" min="0.0" label="Predetermined evolutionary rate for recalibrating synonymous subsitutions (ks) of species" />
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97 <conditional name="codeml_ctl_file_cond">
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98 <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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99 <option value="no" selected="true">No</option>
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100 <option value="yes">Yes</option>
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101 </param>
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102 <when value="no" />
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103 <when value="yes">
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104 <param name="codeml_ctl_file" format="txt" type="data" label="PAML codeml control file" />
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105 </when>
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106 </conditional>
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107 <conditional name="fit_components_cond">
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108 <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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109 <option value="no" selected="true">No</option>
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110 <option value="yes">Yes</option>
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111 </param>
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112 <when value="no" />
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113 <when value="yes">
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114 <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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115 <param name="min_ks" type="float" value="0.0" min="0.0" label="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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116 <param name="max_ks" type="float" value="0.0" min="0.0" label="Upper limit of synonymous subsitutions (ks)" help="Excludes likey ancient paralogous pairs" />
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117 </when>
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118 </conditional>
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119 </when>
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120 </conditional>
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121 </inputs>
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122 <outputs>
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123 <data name="output_species1_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}" />
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124 <data name="output_species1_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}" />
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125 <data name="output_species2_fna" format="fasta" label="KaKs analysis (coding sequences) on ${on_string}">
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126 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
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127 </data>
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128 <data name="output_species2_faa" format="fasta" label="KaKs analysis (amino acids) on ${on_string}">
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129 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
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130 </data>
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131 <data name="output_species1_paralog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
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132 <filter>comparison_cond['comparison'] == 'paralogs'</filter>
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133 </data>
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134 <data name="output_species1_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
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135 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
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136 </data>
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137 <data name="output_species2_ortholog" format="tabular" label="KaKs analysis (blastn results) on ${on_string}">
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138 <filter>comparison_cond['comparison'] == 'orthologs'</filter>
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139 </data>
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140 <data name="output_rbhb" format="tabular" label="KaKs analysis (paralogous pairs) on ${on_string}" />
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141 <data name="output_kaks" format="tabular" label="KaKs analysis on ${on_string}" />
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142 <data name="output_components" format="tabular" label="KaKs analysis (significant components in the ks distribution) on ${on_string}">
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143 <filter>options_type[options_type_selector'] == 'advanced' and options_type['fit_components_cond']['fit_components'] == 'yes</filter>
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144 </data>
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145 </outputs>
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146 <tests>
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147 <test>
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148 </test>
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149 </tests>
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150 <help>
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151 This tool is one of the PlantTribes' collection of automated modular analysis pipelines that utilize objective classifications of
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152 complete protein sequences from sequenced plant genomes to perform comparative evolutionary studies. This tool performs orthologous
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153 or paralogous ks analyses of coding sequences and amino acid sequences.
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154
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155 -----
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156
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157 **Options**
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158
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159 * **Required options**
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160
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161 - **Select gene family clusters** - Sequences classified into gene family clusters, optionally including corresponding coding sequences.
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162 - **Orthogroups or gene families proteins scaffold** - PlantTribes scaffolds data.
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163 - **Protein clustering method** - One of GFam (domain architecture based clustering), OrthoFinder (broadly defined clusters) or OrthoMCL (narrowly defined clusters).
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164
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165 * **Multiple sequence alignments options**
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166
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167 - **Select method for multiple sequence alignments** - Method used for setting multiple sequence alignments.
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168 - **Input sequences include corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs'.
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169 - **Construct orthogroup multiple codon alignments?** - Construct orthogroup multiple codon alignments.
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170 - **Sequence type used in the phylogenetic inference** - Sequence type (dna or amino acid) used in the phylogenetic inference.
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171 - **Use corresponding coding sequences?** - Selecting 'Yes' for this option requires that the selected input data format is 'ptorthocs' or this tool will produce an error.
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172
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173 * **Phylogenetic trees options**
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174
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175 - **Phylogenetic trees inference method** - Phylogenetic trees inference method.
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176 - **Select rooting order configuration for rooting trees??** - If 'No' is selected, trees will be rooted using the most distant taxon present in the orthogroup.
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177 - **Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree** - Number of replicates for rapid bootstrap analysis and search for the best-scoring ML tree.
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178 - **Maximum number of sequences in orthogroup alignments** - Maximum number of sequences in orthogroup alignments.
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179 - **Minimum number of sequences in orthogroup alignments** - Minimum number of sequences in orthogroup alignments.
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180
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181 * **MSA quality control options**
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182
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183 - **Remove sequences with gaps of** - Removes gappy sequences in alignments (i.e., 0.5 removes sequences with 50% gaps).
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184 - **Select process used for gap trimming** - Either nucleotide based trimming or alignments are trimed using using trimAl's ML heuristic trimming approach.
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185 - **Remove sites in alignments with gaps of** - If the process used for gap trimming is nucleotide based, this is the gap value used when removing gappy sites in alignments (i.e., 0.1 removes sites with 90% gaps).
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186
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187 </help>
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188 <citations>
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189 <citation type="bibtex">
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190 @unpublished{None,
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191 author = {Eric Wafula},
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192 title = {None},
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193 year = {None},
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194 url = {https://github.com/dePamphilis/PlantTribes}
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195 }
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196 </citation>
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197 <citation type="doi">10.1186/1471-2105-10-421</citation>
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198 <citation type="doi">10.1093/molbev/msm088</citation>
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199 <citation type="doi">10.18637/jss.v004.i02</citation>
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200 </citations>
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201 </tool>
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