Mercurial > repos > peterjc > blast_rbh

annotate tools/blast_rbh/blast_rbh.xml @ 33:692366540172 draft

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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh commit 21f6d9932d322034e4cea5fee23b24bf0b1e1e85-dirty
author peterjc
date Thu, 18 May 2017 12:43:55 -0400
parents b662383a4bdc
children 5c78f5e6cdf2
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692366540172 planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh commit 21f6d9932d322034e4cea5fee23b24bf0b1e1e85-dirty
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1 <tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.12">
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2 <description>from two FASTA files</description>
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3 <requirements>
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4 <requirement type="package" version="1.67">biopython</requirement>
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5 <requirement type="package" version="2.5.0">blast</requirement>
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6 </requirements>
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7 <version_command>
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8 python $__tool_directory__/blast_rbh.py --version
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9 </version_command>
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10 <command detect_errors="aggressive">
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11 python $__tool_directory__/blast_rbh.py '$fasta_a' '$fasta_b'
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12 -a $seq.dbtype
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13 #if $seq.dbtype=="nucl"
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14 -t $seq.nucl_type
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15 #else
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16 -t $seq.prot_type
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17 #end if
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18 $make_nr
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19 -i $identity
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20 -c $q_cover
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21 -o '$output'
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22 </command>
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23 <inputs>
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24 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->
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25 <param name="fasta_a" type="data" format="fasta"
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26 label="Genes/proteins from species A"
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27 help="FASTA file, one sequence per gene/protein."/>
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28 <param name="fasta_b" type="data" format="fasta"
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29 label="Genes/proteins from species B"
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30 help="FASTA file, one sequence per gene/protein."/>
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31 <conditional name="seq">
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32 <param name="dbtype" type="select" label="Molecule type of FASTA inputs">
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33 <option value="prot">protein</option>
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34 <option value="nucl">nucleotide</option>
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35 </param>
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36 <when value="prot">
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37 <param name="prot_type" type="select" display="radio" label="Type of BLAST">
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38 <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</option>
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39 <option value="blastp-fast">blastp-fast - Uses longer words as described by Shiryev et al (2007)</option>
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40 <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</option>
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41 </param>
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42 </when>
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43 <when value="nucl">
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44 <param name="nucl_type" type="select" display="radio" label="Type of BLAST">
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45 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option>
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46 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option>
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47 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option>
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48 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option>
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49 <option value="tblastx">tblastx - TBLASTX program using translated query against translated database (protein level matches)</option>
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50 </param>
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51 </when>
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52 </conditional>
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53 <param name="identity" type="float" value="70" min="0" max="100"
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54 label="Minimum percentage identity for BLAST matches"
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55 help="Default is 70%, use 0 for no filtering." />
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56 <param name="q_cover" type="float" value="50" min="0" max="100"
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57 label="Minimum percentage query coverage for BLAST matches"
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58 help="Default is 50%, use 0 for no filtering." />
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59 <param name="make_nr" type="boolean" checked="false" truevalue="--nr" falsevalue=""
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60 label="Process input FASTA files to collapse identical sequences"
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61 help="i.e. First make the input non-redundant" />
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62 </inputs>
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63 <outputs>
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64 <data name="output" format="tabular" label="BLAST RBH: $fasta_a.name vs $fasta_b.name" />
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65 </outputs>
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66 <tests>
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67 <test>
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68 <param name="fasta_a" value="four_human_proteins.fasta" ftype="fasta"/>
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69 <param name="fasta_b" value="rhodopsin_proteins.fasta" ftype="fasta"/>
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70 <param name="dbtype" value="prot"/>
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71 <param name="nucl_type" value="blastp"/>
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72 <param name="identity" value="0.0"/>
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73 <param name="q_cover" value="0.0"/>
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74 <output name="output" file="rbh_blastp_four_human_vs_rhodopsin_proteins.tabular" ftype="tabular"/>
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75 </test>
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76 <test>
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77 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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78 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
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79 <param name="dbtype" value="nucl"/>
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80 <param name="nucl_type" value="megablast"/>
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81 <param name="identity" value="0.0"/>
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82 <param name="q_cover" value="0.0"/>
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83 <output name="output" file="rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/>
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84 </test>
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85 <test>
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86 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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87 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
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88 <param name="dbtype" value="nucl"/>
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89 <param name="nucl_type" value="megablast"/>
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90 <param name="identity" value="92"/>
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91 <param name="q_cover" value="86"/>
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92 <output name="output" file="rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/>
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93 </test>
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94 <!-- push the percentage identity over the 92.07% level -->
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95 <test>
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96 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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97 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
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98 <param name="dbtype" value="nucl"/>
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99 <param name="nucl_type" value="megablast"/>
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100 <param name="identity" value="92.5"/>
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101 <param name="q_cover" value="86"/>
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102 <output name="output" file="rbh_none.tabular" ftype="tabular"/>
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103 </test>
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104 <!-- push the coverage over the 86% level -->
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105 <test>
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106 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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107 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
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108 <param name="dbtype" value="nucl"/>
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109 <param name="nucl_type" value="megablast"/>
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110 <param name="identity" value="92"/>
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111 <param name="q_cover" value="87"/>
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112 <output name="output" file="rbh_none.tabular" ftype="tabular"/>
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113 </test>
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114 <test>
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115 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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116 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
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117 <param name="dbtype" value="nucl"/>
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118 <param name="nucl_type" value="tblastx"/>
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119 <param name="identity" value="0.0"/>
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120 <param name="q_cover" value="0.0"/>
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121 <output name="output" file="rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/>
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122 </test>
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123 <test>
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124 <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta"/>
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125 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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126 <param name="dbtype" value="nucl"/>
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127 <param name="nucl_type" value="blastn"/>
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128 <param name="identity" value="0.0"/>
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129 <param name="q_cover" value="0.0"/>
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130 <output name="output" file="rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular" ftype="tabular"/>
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131 </test>
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132 <!-- this pair of examples test tied best hits -->
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133 <test>
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134 <param name="fasta_a" value="k12_ten_proteins.fasta" ftype="fasta"/>
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135 <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/>
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136 <param name="dbtype" value="prot"/>
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137 <param name="nucl_type" value="blastp"/>
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138 <param name="identity" value="0.0"/>
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139 <param name="q_cover" value="0.0"/>
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140 <output name="output" file="rbh_blastp_k12.tabular" ftype="tabular"/>
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141 </test>
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142 <test>
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143 <param name="fasta_a" value="k12_edited_proteins.fasta" ftype="fasta"/>
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144 <param name="fasta_b" value="k12_ten_proteins.fasta" ftype="fasta"/>
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145 <param name="dbtype" value="prot"/>
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146 <param name="nucl_type" value="blastp"/>
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147 <param name="identity" value="0.0"/>
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148 <param name="q_cover" value="0.0"/>
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149 <output name="output" file="rbh_blastp_k12.tabular" ftype="tabular"/>
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150 </test>
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151 <!-- this tests self-comparison -->
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152 <test>
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153 <param name="fasta_a" value="k12_edited_proteins.fasta" ftype="fasta"/>
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154 <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/>
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155 <param name="dbtype" value="prot"/>
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156 <param name="nucl_type" value="blastp-fast"/>
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157 <param name="identity" value="80.0"/>
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158 <param name="q_cover" value="80.0"/>
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159 <output name="output" file="rbh_blastp_k12_self.tabular" ftype="tabular"/>
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160 </test>
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161 </tests>
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162 <help>
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163 **What it does**
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164
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165 Takes two FASTA files (*species A* and *species B*), builds a BLAST database
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166 for each, runs reciprocal BLAST searchs (*A vs B*, and *B vs A*), optionally
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167 filters the HSPs, and then compiles a list of the reciprocal best hits (RBH).
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168
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169 The output from this tool is a tabular file containing multiple columns, with
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170 information about the BLAST matches used:
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171
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172 ====== ==================================
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173 Column Description
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174 ------ ----------------------------------
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175 1 ID from *species A*
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176 2 ID from *species B*
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177 3 Length of sequence *A*
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178 4 Length of sequence *B*
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179 5 Percentage of sequence *A* covered
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180 6 Percentage of sequence *B* covered
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181 7 HSP alignment length
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182 8 HSP percentage identity
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183 9 HSP bitscore
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184 ====== ==================================
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185
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186 These values correspond to the ``qseqid``/``sseqid``, ``qlen``/``slen``,
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187 ``qcovhsp``, ``length``, ``pident`` and ``bitscore`` values in the BLAST+
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188 tabular output.
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189
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190 For the alignment length, bitscore and percentage identity the values for
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191 *A vs B* and *B vs A* are typically the same, so their minimum is shown.
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192 The coverage values are given by the HSP alignment length divided by the
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193 sequence length (adjusted by a factor of three for TBLASTX).
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194
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195 Note that if a sequence has equally scoring top BLAST matches to multiple
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196 sequence in the other file, it will not be considered for an RBH. This
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197 can happen following gene duplication, or for (near) identical gene
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198 duplicates.
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199
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200 The tool can optionally make the FASTA files non-redundant by replacing
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201 repeated identical sequences with a single representative before building
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202 the databases and running BLAST.
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203
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204 Finally, the tool can be run using the same FASTA input file to look for
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205 RBH within the dataset. In this case, self matches are discarded.
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206
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207 .. class:: warningmark
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208
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209 **Note**
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210
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211 If you are trying to use BLAST RBH matches to identify candidate orthologues
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212 or transfer annotation, you *must* use a percentage identity and minimum
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213 coverage threshold or similiar. See:
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214
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215 Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction,
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216 or How To Use Sequence and Structure Information To Predict Protein
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217 Function. PLoS Comput Biol 4(10): e1000160.
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218 http://dx.doi.org/10.1371/journal.pcbi.1000160
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219
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220 The defaults are to require 70% sequence identity over the aligned region
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221 (using ``pident`` in the BLAST+ tabular output), and that the HSP alignment
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222 covers at least 50% of the query sequence (using ``qcovhsp`` in the BLAST+
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223 tabular output).
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224
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225
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226 **References**
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227
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228 Please cite:
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229
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230 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo (2015).
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231 NCBI BLAST+ integrated into Galaxy.
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232 *GigaScience* 4:39
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233 http://dx.doi.org/10.1186/s13742-015-0080-7
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234
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235 Christiam Camacho et al. (2009).
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236 BLAST+: architecture and applications.
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237 *BMC Bioinformatics* 15;10:421.
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238 http://dx.doi.org/10.1186/1471-2105-10-421
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239
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240 This wrapper is available to install into other Galaxy Instances via the Galaxy
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241 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
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242 </help>
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243 <citations>
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244 <citation type="doi">10.1186/1471-2105-10-421</citation>
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245 <citation type="doi">10.1186/s13742-015-0080-7</citation>
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246 </citations>
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247 </tool>