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1 <tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.0">
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2 <description>from two FASTA files</description>
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3 <requirements>
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4 <requirement type="binary">makeblastdb</requirement>
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5 <requirement type="binary">blastp</requirement>
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6 <requirement type="binary">blastn</requirement>
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7 <requirement type="package" version="2.2.29">blast+</requirement>
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8 </requirements>
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9 <version_command interpreter="python">
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10 blast_rbh.py --version
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11 </version_command>
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12 <command interpreter="python">
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13 blast_rbh.py "$fasta_a" "$fasta_b" $seq.dbtype
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14 #if $seq.dbtype=="nucl"
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15 $seq.nucl_type
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16 #else
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17 $seq.prot_type
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18 #end if
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19 $identity $q_cover "$output"
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20 </command>
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21 <inputs>
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22 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA -->
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23 <param name="fasta_a" type="data" format="fasta"
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24 label="Genes/proteins from species A"
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25 description="FASTA file, one sequence per gene/protein." />
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26 <param name="fasta_b" type="data" format="fasta"
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27 label="Genes/proteins from species B"
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28 description="FASTA file, one sequence per gene/protein." />
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29 <conditional name="seq">
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30 <param name="dbtype" type="select" label="Molecule type of FASTA inputs">
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31 <option value="prot">protein</option>
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32 <option value="nucl">nucleotide</option>
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33 </param>
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34 <when value="prot">
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35 <param name="prot_type" type="select" display="radio" label="Type of BLAST">
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36 <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</option>
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37 <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</option>
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38 </param>
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39 </when>
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40 <when value="nucl">
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41 <param name="nucl_type" type="select" display="radio" label="Type of BLAST">
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42 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option>
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43 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option>
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44 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option>
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45 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option>
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46 </param>
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47 </when>
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48 </conditional>
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49 <param name="identity" type="float" value="70" min="0" max="100"
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50 label="Minimum percentage identity for BLAST matches"
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51 help="Default is 70%, use 0 for no filtering." />
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52 <param name="q_cover" type="float" value="50" min="0" max="100"
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53 label="Minimum percentage query coverage for BLAST matches"
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54 help="Default is 50%, use 0 for no filtering." />
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55 </inputs>
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56 <outputs>
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57 <data name="output" format="tabular" label="BLAST RBH: $fasta_a.name vs $fasta_b.name" />
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58 </outputs>
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59 <requirements>
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60 </requirements>
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61 <tests>
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62 <test>
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1
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63 <param name="fasta_a" value="four_human_proteins.fasta" ftype="fasta"/>
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64 <param name="fasta_b" value="rhodopsin_proteins.fasta" ftype="fasta"/>
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65 <param name="dbtype" value="prot"/>
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66 <param name="nucl_type" value="blastp"/>
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67 <param name="identity" value="0.0"/>
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68 <param name="q_cover" value="0.0"/>
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69 <output name="output" file="rbh_blastp_four_human_vs_rhodopsin_proteins.tabular" ftype="tabular"/>
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70 </test>
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71 <test>
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0
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72 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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73 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
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74 <param name="dbtype" value="nucl"/>
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75 <param name="nucl_type" value="megablast"/>
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76 <param name="identity" value="0.0"/>
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77 <param name="q_cover" value="0.0"/>
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78 <output name="output" file="rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/>
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79 </test>
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80 <test>
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81 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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82 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
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83 <param name="dbtype" value="nucl"/>
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84 <param name="nucl_type" value="megablast"/>
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85 <param name="identity" value="92"/>
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86 <param name="q_cover" value="86"/>
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87 <output name="output" file="rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/>
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88 </test>
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89 <!-- push the percentage identity over the 92.07% level -->
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90 <test>
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91 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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92 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
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93 <param name="dbtype" value="nucl"/>
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94 <param name="nucl_type" value="megablast"/>
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95 <param name="identity" value="92.5"/>
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96 <param name="q_cover" value="86"/>
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97 <output name="output" file="rbh_none.tabular" ftype="tabular"/>
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98 </test>
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99 <!-- push the coverage over the 86% level -->
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100 <test>
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101 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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102 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/>
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103 <param name="dbtype" value="nucl"/>
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104 <param name="nucl_type" value="megablast"/>
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105 <param name="identity" value="92"/>
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106 <param name="q_cover" value="87"/>
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107 <output name="output" file="rbh_none.tabular" ftype="tabular"/>
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108 </test>
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109 <test>
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110 <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta"/>
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111 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta"/>
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112 <param name="dbtype" value="nucl"/>
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113 <param name="nucl_type" value="blastn"/>
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114 <param name="identity" value="0.0"/>
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115 <param name="q_cover" value="0.0"/>
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116 <output name="output" file="rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular" ftype="tabular"/>
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117 </test>
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118 </tests>
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119 <help>
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120 **What it does**
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121
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2
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122 Takes two FASTA files (*species A* and *species B*), builds a BLAST database
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123 for each, runs reciprocal BLAST searchs (*A vs B*, and *B vs A*), optionally
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2
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124 filters the HSPs, and then compiles a list of the reciprocal best hits (RBH).
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125
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126 The output from this tool is a tabular file containing eight columns, with
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127 information about the BLAST matches used:
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128
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129 ====== =================================
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130 Column Description
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131 ------ ---------------------------------
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132 1 ID from *species A*
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133 2 ID from *species B*
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134 3 Bitscore from *A vs B*
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2
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135 4 Percentage identity from *A vs B*
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136 5 Query coverage from *A vs B*
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137 6 Bitscore from *B vs A*
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138 7 Percentage identity from *B vs A*
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139 8 Query coverage from *B vs A*
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140 ====== =================================
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141
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142 These values correspond to the ``bitscore``, ``pident`` and ``qcovhsp``
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143 values in the BLAST+ tabular output.
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144
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145 .. class:: warningmark
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146
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147 **Note**
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148
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149 If you are trying to use BLAST RBH matches to identify candidate orthologues
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150 or transfer annotation, you *must* use a percentage identity and minimum
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151 coverage threshold or similiar. See:
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152
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153 Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction,
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154 or How To Use Sequence and Structure Information To Predict Protein
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155 Function. PLoS Comput Biol 4(10): e1000160.
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156 http://dx.doi.org/10.1371/journal.pcbi.1000160
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157
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158 The defaults are to require 70% sequence identity over the aligned region
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159 (using ``pident`` in the BLAST+ tabular output), and that the HSP alignment
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160 covers at least 50% of the query sequence (using ``qcovhsp`` in the BLAST+
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161 tabular output).
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162
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163
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164 **References**
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165
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166 A specific paper covering this tool is planned, but please also cite:
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167
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168 Christiam Camacho et al. (2009).
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169 BLAST+: architecture and applications.
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170 BMC Bioinformatics. 15;10:421.
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171 http://dx.doi.org/10.1186/1471-2105-10-421
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172
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173 This wrapper is available to install into other Galaxy Instances via the Galaxy
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174 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh
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175 </help>
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176 </tool>
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