Mercurial > repos > peterjc > blast_rbh
annotate tools/blast_rbh/blast_rbh.xml @ 20:e8f8c580bcca draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast_rbh commit 05c2a834609f1fd02372c4f9b0a0733680fe9675-dirty
| author | peterjc |
|---|---|
| date | Fri, 15 May 2015 05:47:40 -0400 |
| parents | b6531758b428 |
| children | b41f8c43705e |
| rev | line source |
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planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast_rbh commit 05c2a834609f1fd02372c4f9b0a0733680fe9675-dirty
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1 <tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.7"> |
| 0 | 2 <description>from two FASTA files</description> |
| 3 <requirements> | |
| 12 | 4 <requirement type="package" version="1.64">biopython</requirement> |
| 5 <requirement type="python-module">Bio</requirement> | |
| 6 <requirement type="binary">makeblastdb</requirement> | |
| 7 <requirement type="binary">blastp</requirement> | |
| 8 <requirement type="binary">blastn</requirement> | |
| 13 | 9 <requirement type="package" version="2.2.30">blast+</requirement> |
| 0 | 10 </requirements> |
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planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast_rbh commit 05c2a834609f1fd02372c4f9b0a0733680fe9675-dirty
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11 <stdio> |
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12 <!-- Anything other than zero is an error --> |
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planemo upload for repository https://github.com/peterjc/galaxy_blast/tools/blast_rbh commit 05c2a834609f1fd02372c4f9b0a0733680fe9675-dirty
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13 <exit_code range="1:" /> |
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14 <exit_code range=":-1" /> |
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15 </stdio> |
| 0 | 16 <version_command interpreter="python"> |
| 17 blast_rbh.py --version | |
| 18 </version_command> | |
| 19 <command interpreter="python"> | |
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20 blast_rbh.py "$fasta_a" "$fasta_b" |
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21 -a $seq.dbtype |
| 0 | 22 #if $seq.dbtype=="nucl" |
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23 -t $seq.nucl_type |
| 0 | 24 #else |
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25 -t $seq.prot_type |
| 0 | 26 #end if |
| 12 | 27 $make_nr |
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28 -i $identity |
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29 -c $q_cover |
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30 -o "$output" |
| 0 | 31 </command> |
| 32 <inputs> | |
| 33 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> | |
| 34 <param name="fasta_a" type="data" format="fasta" | |
| 35 label="Genes/proteins from species A" | |
| 36 description="FASTA file, one sequence per gene/protein." /> | |
| 37 <param name="fasta_b" type="data" format="fasta" | |
| 38 label="Genes/proteins from species B" | |
| 39 description="FASTA file, one sequence per gene/protein." /> | |
| 40 <conditional name="seq"> | |
| 41 <param name="dbtype" type="select" label="Molecule type of FASTA inputs"> | |
| 42 <option value="prot">protein</option> | |
| 43 <option value="nucl">nucleotide</option> | |
| 44 </param> | |
| 45 <when value="prot"> | |
| 46 <param name="prot_type" type="select" display="radio" label="Type of BLAST"> | |
| 47 <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</option> | |
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48 <option value="blastp-fast">blastp-fast - Uses longer words as described by Shiryev et al (2007)</option> |
| 0 | 49 <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</option> |
| 50 </param> | |
| 51 </when> | |
| 52 <when value="nucl"> | |
| 53 <param name="nucl_type" type="select" display="radio" label="Type of BLAST"> | |
| 54 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option> | |
| 55 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option> | |
| 56 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option> | |
| 57 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option> | |
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58 <option value="tblastx">tblastx - TBLASTX program using translated query against translated database (protein level matches)</option> |
| 0 | 59 </param> |
| 60 </when> | |
| 61 </conditional> | |
| 62 <param name="identity" type="float" value="70" min="0" max="100" | |
| 63 label="Minimum percentage identity for BLAST matches" | |
| 64 help="Default is 70%, use 0 for no filtering." /> | |
| 65 <param name="q_cover" type="float" value="50" min="0" max="100" | |
| 66 label="Minimum percentage query coverage for BLAST matches" | |
| 67 help="Default is 50%, use 0 for no filtering." /> | |
| 12 | 68 <param name="make_nr" type="boolean" checked="false" truevalue="--nr" falsevalue="" |
| 69 label="Process input FASTA files to collapse identical sequences" | |
| 70 help="i.e. First make the input non-redundant" /> | |
| 0 | 71 </inputs> |
| 72 <outputs> | |
| 73 <data name="output" format="tabular" label="BLAST RBH: $fasta_a.name vs $fasta_b.name" /> | |
| 74 </outputs> | |
| 75 <tests> | |
| 76 <test> | |
| 1 | 77 <param name="fasta_a" value="four_human_proteins.fasta" ftype="fasta"/> |
| 78 <param name="fasta_b" value="rhodopsin_proteins.fasta" ftype="fasta"/> | |
| 79 <param name="dbtype" value="prot"/> | |
| 80 <param name="nucl_type" value="blastp"/> | |
| 81 <param name="identity" value="0.0"/> | |
| 82 <param name="q_cover" value="0.0"/> | |
| 83 <output name="output" file="rbh_blastp_four_human_vs_rhodopsin_proteins.tabular" ftype="tabular"/> | |
| 84 </test> | |
| 85 <test> | |
| 0 | 86 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> |
| 87 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> | |
| 88 <param name="dbtype" value="nucl"/> | |
| 89 <param name="nucl_type" value="megablast"/> | |
| 90 <param name="identity" value="0.0"/> | |
| 91 <param name="q_cover" value="0.0"/> | |
| 92 <output name="output" file="rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/> | |
| 93 </test> | |
| 94 <test> | |
| 95 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> | |
| 96 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> | |
| 97 <param name="dbtype" value="nucl"/> | |
| 98 <param name="nucl_type" value="megablast"/> | |
| 99 <param name="identity" value="92"/> | |
| 100 <param name="q_cover" value="86"/> | |
| 101 <output name="output" file="rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/> | |
| 102 </test> | |
| 103 <!-- push the percentage identity over the 92.07% level --> | |
| 104 <test> | |
| 105 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> | |
| 106 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> | |
| 107 <param name="dbtype" value="nucl"/> | |
| 108 <param name="nucl_type" value="megablast"/> | |
| 109 <param name="identity" value="92.5"/> | |
| 110 <param name="q_cover" value="86"/> | |
| 111 <output name="output" file="rbh_none.tabular" ftype="tabular"/> | |
| 112 </test> | |
| 113 <!-- push the coverage over the 86% level --> | |
| 114 <test> | |
| 115 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> | |
| 116 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> | |
| 117 <param name="dbtype" value="nucl"/> | |
| 118 <param name="nucl_type" value="megablast"/> | |
| 119 <param name="identity" value="92"/> | |
| 120 <param name="q_cover" value="87"/> | |
| 121 <output name="output" file="rbh_none.tabular" ftype="tabular"/> | |
| 122 </test> | |
| 123 <test> | |
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124 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> |
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125 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> |
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126 <param name="dbtype" value="nucl"/> |
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127 <param name="nucl_type" value="tblastx"/> |
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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_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/> |
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131 </test> |
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132 <test> |
| 0 | 133 <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta"/> |
| 134 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta"/> | |
| 135 <param name="dbtype" value="nucl"/> | |
| 136 <param name="nucl_type" value="blastn"/> | |
| 137 <param name="identity" value="0.0"/> | |
| 138 <param name="q_cover" value="0.0"/> | |
| 139 <output name="output" file="rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular" ftype="tabular"/> | |
| 140 </test> | |
| 6 | 141 <!-- this pair of examples test tied best hits --> |
| 142 <test> | |
| 143 <param name="fasta_a" value="k12_ten_proteins.fasta" ftype="fasta"/> | |
| 144 <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/> | |
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145 <param name="dbtype" value="prot"/> |
| 6 | 146 <param name="nucl_type" value="blastp"/> |
| 147 <param name="identity" value="0.0"/> | |
| 148 <param name="q_cover" value="0.0"/> | |
| 149 <output name="output" file="rbh_blastp_k12.tabular" ftype="tabular"/> | |
| 150 </test> | |
| 151 <test> | |
| 152 <param name="fasta_a" value="k12_edited_proteins.fasta" ftype="fasta"/> | |
| 153 <param name="fasta_b" value="k12_ten_proteins.fasta" ftype="fasta"/> | |
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154 <param name="dbtype" value="prot"/> |
| 6 | 155 <param name="nucl_type" value="blastp"/> |
| 156 <param name="identity" value="0.0"/> | |
| 157 <param name="q_cover" value="0.0"/> | |
| 158 <output name="output" file="rbh_blastp_k12.tabular" ftype="tabular"/> | |
| 159 </test> | |
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160 <!-- this tests self-comparison --> |
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161 <test> |
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162 <param name="fasta_a" value="k12_edited_proteins.fasta" ftype="fasta"/> |
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163 <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/> |
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164 <param name="dbtype" value="prot"/> |
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165 <param name="nucl_type" value="blastp-fast"/> |
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166 <param name="identity" value="80.0"/> |
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167 <param name="q_cover" value="80.0"/> |
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168 <output name="output" file="rbh_blastp_k12_self.tabular" ftype="tabular"/> |
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169 </test> |
| 0 | 170 </tests> |
| 171 <help> | |
| 172 **What it does** | |
| 173 | |
| 2 | 174 Takes two FASTA files (*species A* and *species B*), builds a BLAST database |
| 0 | 175 for each, runs reciprocal BLAST searchs (*A vs B*, and *B vs A*), optionally |
| 2 | 176 filters the HSPs, and then compiles a list of the reciprocal best hits (RBH). |
| 0 | 177 |
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178 The output from this tool is a tabular file containing multiple columns, with |
| 2 | 179 information about the BLAST matches used: |
| 0 | 180 |
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181 ====== ================================== |
| 0 | 182 Column Description |
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183 ------ ---------------------------------- |
| 2 | 184 1 ID from *species A* |
| 185 2 ID from *species B* | |
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186 3 Length of sequence *A* |
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187 4 Length of sequence *B* |
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188 5 Percentage of sequence *A* covered |
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189 6 Percentage of sequence *B* covered |
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190 7 HSP alignment length |
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191 8 HSP percentage identity |
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192 9 HSP bitscore |
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193 ====== ================================== |
| 2 | 194 |
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195 These values correspond to the ``qseqid``/``sseqid``, ``qlen``/``slen``, |
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196 ``qcovhsp``, ``length``, ``pident`` and ``bitscore`` values in the BLAST+ |
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197 tabular output. |
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198 |
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199 For the alignment length, bitscore and percentage identity the values for |
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200 *A vs B* and *B vs A* are typically the same, so their minimum is shown. |
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201 The coverage values are given by the HSP alignment length divided by the |
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202 sequence length (adjusted by a factor of three for TBLASTX). |
| 0 | 203 |
| 6 | 204 Note that if a sequence has equally scoring top BLAST matches to multiple |
| 205 sequence in the other file, it will not be considered for an RBH. This | |
| 206 can happen following gene duplication, or for (near) identical gene | |
| 207 duplicates. | |
| 208 | |
| 12 | 209 The tool can optionally make the FASTA files non-redundant by replacing |
| 210 repeated identical sequences with a single representative before building | |
| 211 the databases and running BLAST. | |
| 212 | |
| 213 Finally, the tool can be run using the same FASTA input file to look for | |
| 214 RBH within the dataset. In this case, self matches are discarded. | |
| 215 | |
| 0 | 216 .. class:: warningmark |
| 217 | |
| 218 **Note** | |
| 219 | |
| 220 If you are trying to use BLAST RBH matches to identify candidate orthologues | |
| 221 or transfer annotation, you *must* use a percentage identity and minimum | |
| 222 coverage threshold or similiar. See: | |
| 223 | |
| 224 Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction, | |
| 225 or How To Use Sequence and Structure Information To Predict Protein | |
| 226 Function. PLoS Comput Biol 4(10): e1000160. | |
| 227 http://dx.doi.org/10.1371/journal.pcbi.1000160 | |
| 228 | |
| 229 The defaults are to require 70% sequence identity over the aligned region | |
| 230 (using ``pident`` in the BLAST+ tabular output), and that the HSP alignment | |
| 231 covers at least 50% of the query sequence (using ``qcovhsp`` in the BLAST+ | |
| 232 tabular output). | |
| 233 | |
| 234 | |
| 235 **References** | |
| 236 | |
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237 Please cite: |
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238 |
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239 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo (2015). |
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240 NCBI BLAST+ integrated into Galaxy. |
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241 bioRxiv prepint. |
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242 http://dx.doi.org/10.1101/014043 |
| 0 | 243 |
| 244 Christiam Camacho et al. (2009). | |
| 245 BLAST+: architecture and applications. | |
| 246 BMC Bioinformatics. 15;10:421. | |
| 247 http://dx.doi.org/10.1186/1471-2105-10-421 | |
| 248 | |
| 249 This wrapper is available to install into other Galaxy Instances via the Galaxy | |
| 250 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh | |
| 251 </help> | |
| 10 | 252 <citations> |
| 253 <citation type="doi">10.1186/1471-2105-10-421</citation> | |
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254 <citation type="doi">10.1101/014043</citation> |
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255 <!-- TODO - Update once "NCBI BLAST+ integrated into Galaxy" formally published --> |
| 10 | 256 </citations> |
| 0 | 257 </tool> |