Mercurial > repos > peterjc > blast_rbh
annotate tools/blast_rbh/blast_rbh.xml @ 32:b662383a4bdc draft
planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh commit 39737c01a51469d0cf9920273de6c151ba84048d-dirty
| author | peterjc |
|---|---|
| date | Thu, 18 May 2017 07:39:37 -0400 |
| parents | a168be0dbd4f |
| children | 692366540172 |
| rev | line source |
|---|---|
| 28 | 1 <tool id="blast_reciprocal_best_hits" name="BLAST Reciprocal Best Hits (RBH)" version="0.1.11"> |
| 0 | 2 <description>from two FASTA files</description> |
| 3 <requirements> | |
| 28 | 4 <requirement type="package" version="1.67">biopython</requirement> |
| 5 <requirement type="package" version="2.5.0">blast</requirement> | |
| 0 | 6 </requirements> |
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7 <stdio> |
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8 <!-- Anything other than zero is an error --> |
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9 <exit_code range="1:" /> |
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10 <exit_code range=":-1" /> |
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11 </stdio> |
| 0 | 12 <version_command interpreter="python"> |
| 13 blast_rbh.py --version | |
| 14 </version_command> | |
| 15 <command interpreter="python"> | |
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16 blast_rbh.py "$fasta_a" "$fasta_b" |
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17 -a $seq.dbtype |
| 0 | 18 #if $seq.dbtype=="nucl" |
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19 -t $seq.nucl_type |
| 0 | 20 #else |
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21 -t $seq.prot_type |
| 0 | 22 #end if |
| 12 | 23 $make_nr |
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24 -i $identity |
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25 -c $q_cover |
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26 -o "$output" |
| 0 | 27 </command> |
| 28 <inputs> | |
| 29 <!-- Galaxy does not have sub-types for protein vs nucletide FASTA --> | |
| 30 <param name="fasta_a" type="data" format="fasta" | |
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31 label="Genes/proteins from species A" |
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32 help="FASTA file, one sequence per gene/protein."/> |
| 0 | 33 <param name="fasta_b" type="data" format="fasta" |
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34 label="Genes/proteins from species B" |
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35 help="FASTA file, one sequence per gene/protein."/> |
| 0 | 36 <conditional name="seq"> |
| 37 <param name="dbtype" type="select" label="Molecule type of FASTA inputs"> | |
| 38 <option value="prot">protein</option> | |
| 39 <option value="nucl">nucleotide</option> | |
| 40 </param> | |
| 41 <when value="prot"> | |
| 42 <param name="prot_type" type="select" display="radio" label="Type of BLAST"> | |
| 43 <option value="blastp">blastp - Traditional BLASTP to compare a protein query to a protein database</option> | |
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44 <option value="blastp-fast">blastp-fast - Uses longer words as described by Shiryev et al (2007)</option> |
| 0 | 45 <option value="blastp-short">blastp-short - BLASTP optimized for queries shorter than 30 residues</option> |
| 46 </param> | |
| 47 </when> | |
| 48 <when value="nucl"> | |
| 49 <param name="nucl_type" type="select" display="radio" label="Type of BLAST"> | |
| 50 <option value="megablast">megablast - Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences</option> | |
| 51 <option value="blastn">blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences</option> | |
| 52 <option value="blastn-short">blastn-short - BLASTN program optimized for sequences shorter than 50 bases</option> | |
| 53 <option value="dc-megablast">dc-megablast - Discontiguous megablast used to find more distant (e.g., interspecies) sequences</option> | |
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54 <option value="tblastx">tblastx - TBLASTX program using translated query against translated database (protein level matches)</option> |
| 0 | 55 </param> |
| 56 </when> | |
| 57 </conditional> | |
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58 <param name="identity" type="float" value="70" min="0" max="100" |
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59 label="Minimum percentage identity for BLAST matches" |
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60 help="Default is 70%, use 0 for no filtering." /> |
| 0 | 61 <param name="q_cover" type="float" value="50" min="0" max="100" |
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62 label="Minimum percentage query coverage for BLAST matches" |
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planemo upload for repository https://github.com/peterjc/galaxy_blast/tree/master/tools/blast_rbh commit 39737c01a51469d0cf9920273de6c151ba84048d-dirty
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63 help="Default is 50%, use 0 for no filtering." /> |
| 12 | 64 <param name="make_nr" type="boolean" checked="false" truevalue="--nr" falsevalue="" |
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65 label="Process input FASTA files to collapse identical sequences" |
| 12 | 66 help="i.e. First make the input non-redundant" /> |
| 0 | 67 </inputs> |
| 68 <outputs> | |
| 69 <data name="output" format="tabular" label="BLAST RBH: $fasta_a.name vs $fasta_b.name" /> | |
| 70 </outputs> | |
| 71 <tests> | |
| 72 <test> | |
| 1 | 73 <param name="fasta_a" value="four_human_proteins.fasta" ftype="fasta"/> |
| 74 <param name="fasta_b" value="rhodopsin_proteins.fasta" ftype="fasta"/> | |
| 75 <param name="dbtype" value="prot"/> | |
| 76 <param name="nucl_type" value="blastp"/> | |
| 77 <param name="identity" value="0.0"/> | |
| 78 <param name="q_cover" value="0.0"/> | |
| 79 <output name="output" file="rbh_blastp_four_human_vs_rhodopsin_proteins.tabular" ftype="tabular"/> | |
| 80 </test> | |
| 81 <test> | |
| 0 | 82 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> |
| 83 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> | |
| 84 <param name="dbtype" value="nucl"/> | |
| 85 <param name="nucl_type" value="megablast"/> | |
| 86 <param name="identity" value="0.0"/> | |
| 87 <param name="q_cover" value="0.0"/> | |
| 88 <output name="output" file="rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/> | |
| 89 </test> | |
| 90 <test> | |
| 91 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> | |
| 92 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> | |
| 93 <param name="dbtype" value="nucl"/> | |
| 94 <param name="nucl_type" value="megablast"/> | |
| 95 <param name="identity" value="92"/> | |
| 96 <param name="q_cover" value="86"/> | |
| 97 <output name="output" file="rbh_megablast_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/> | |
| 98 </test> | |
| 99 <!-- push the percentage identity over the 92.07% level --> | |
| 100 <test> | |
| 101 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> | |
| 102 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> | |
| 103 <param name="dbtype" value="nucl"/> | |
| 104 <param name="nucl_type" value="megablast"/> | |
| 105 <param name="identity" value="92.5"/> | |
| 106 <param name="q_cover" value="86"/> | |
| 107 <output name="output" file="rbh_none.tabular" ftype="tabular"/> | |
| 108 </test> | |
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109 <!-- push the coverage over the 86% level --> |
| 0 | 110 <test> |
| 111 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> | |
| 112 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> | |
| 113 <param name="dbtype" value="nucl"/> | |
| 114 <param name="nucl_type" value="megablast"/> | |
| 115 <param name="identity" value="92"/> | |
| 116 <param name="q_cover" value="87"/> | |
| 117 <output name="output" file="rbh_none.tabular" ftype="tabular"/> | |
| 118 </test> | |
| 119 <test> | |
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120 <param name="fasta_a" value="rhodopsin_nucs.fasta" ftype="fasta"/> |
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121 <param name="fasta_b" value="three_human_mRNA.fasta" ftype="fasta"/> |
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122 <param name="dbtype" value="nucl"/> |
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123 <param name="nucl_type" value="tblastx"/> |
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124 <param name="identity" value="0.0"/> |
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125 <param name="q_cover" value="0.0"/> |
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126 <output name="output" file="rbh_tblastx_rhodopsin_nucs_vs_three_human_mRNA.tabular" ftype="tabular"/> |
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127 </test> |
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128 <test> |
| 0 | 129 <param name="fasta_a" value="three_human_mRNA.fasta" ftype="fasta"/> |
| 130 <param name="fasta_b" value="rhodopsin_nucs.fasta" ftype="fasta"/> | |
| 131 <param name="dbtype" value="nucl"/> | |
| 132 <param name="nucl_type" value="blastn"/> | |
| 133 <param name="identity" value="0.0"/> | |
| 134 <param name="q_cover" value="0.0"/> | |
| 135 <output name="output" file="rbh_blastn_three_human_mRNA_vs_rhodopsin_nucs.tabular" ftype="tabular"/> | |
| 136 </test> | |
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137 <!-- this pair of examples test tied best hits --> |
| 6 | 138 <test> |
| 139 <param name="fasta_a" value="k12_ten_proteins.fasta" ftype="fasta"/> | |
| 140 <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/> | |
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141 <param name="dbtype" value="prot"/> |
| 6 | 142 <param name="nucl_type" value="blastp"/> |
| 143 <param name="identity" value="0.0"/> | |
| 144 <param name="q_cover" value="0.0"/> | |
| 145 <output name="output" file="rbh_blastp_k12.tabular" ftype="tabular"/> | |
| 146 </test> | |
| 147 <test> | |
| 148 <param name="fasta_a" value="k12_edited_proteins.fasta" ftype="fasta"/> | |
| 149 <param name="fasta_b" value="k12_ten_proteins.fasta" ftype="fasta"/> | |
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150 <param name="dbtype" value="prot"/> |
| 6 | 151 <param name="nucl_type" value="blastp"/> |
| 152 <param name="identity" value="0.0"/> | |
| 153 <param name="q_cover" value="0.0"/> | |
| 154 <output name="output" file="rbh_blastp_k12.tabular" ftype="tabular"/> | |
| 155 </test> | |
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156 <!-- this tests self-comparison --> |
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157 <test> |
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158 <param name="fasta_a" value="k12_edited_proteins.fasta" ftype="fasta"/> |
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159 <param name="fasta_b" value="k12_edited_proteins.fasta" ftype="fasta"/> |
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160 <param name="dbtype" value="prot"/> |
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161 <param name="nucl_type" value="blastp-fast"/> |
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162 <param name="identity" value="80.0"/> |
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163 <param name="q_cover" value="80.0"/> |
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164 <output name="output" file="rbh_blastp_k12_self.tabular" ftype="tabular"/> |
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165 </test> |
| 0 | 166 </tests> |
| 167 <help> | |
| 168 **What it does** | |
| 169 | |
| 2 | 170 Takes two FASTA files (*species A* and *species B*), builds a BLAST database |
| 0 | 171 for each, runs reciprocal BLAST searchs (*A vs B*, and *B vs A*), optionally |
| 2 | 172 filters the HSPs, and then compiles a list of the reciprocal best hits (RBH). |
| 0 | 173 |
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174 The output from this tool is a tabular file containing multiple columns, with |
| 2 | 175 information about the BLAST matches used: |
| 0 | 176 |
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177 ====== ================================== |
| 0 | 178 Column Description |
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179 ------ ---------------------------------- |
| 2 | 180 1 ID from *species A* |
| 181 2 ID from *species B* | |
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182 3 Length of sequence *A* |
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183 4 Length of sequence *B* |
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184 5 Percentage of sequence *A* covered |
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185 6 Percentage of sequence *B* covered |
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186 7 HSP alignment length |
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187 8 HSP percentage identity |
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188 9 HSP bitscore |
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189 ====== ================================== |
| 2 | 190 |
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191 These values correspond to the ``qseqid``/``sseqid``, ``qlen``/``slen``, |
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192 ``qcovhsp``, ``length``, ``pident`` and ``bitscore`` values in the BLAST+ |
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193 tabular output. |
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194 |
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195 For the alignment length, bitscore and percentage identity the values for |
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196 *A vs B* and *B vs A* are typically the same, so their minimum is shown. |
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197 The coverage values are given by the HSP alignment length divided by the |
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198 sequence length (adjusted by a factor of three for TBLASTX). |
| 0 | 199 |
| 6 | 200 Note that if a sequence has equally scoring top BLAST matches to multiple |
| 201 sequence in the other file, it will not be considered for an RBH. This | |
| 202 can happen following gene duplication, or for (near) identical gene | |
| 203 duplicates. | |
| 204 | |
| 12 | 205 The tool can optionally make the FASTA files non-redundant by replacing |
| 206 repeated identical sequences with a single representative before building | |
| 207 the databases and running BLAST. | |
| 208 | |
| 209 Finally, the tool can be run using the same FASTA input file to look for | |
| 210 RBH within the dataset. In this case, self matches are discarded. | |
| 211 | |
| 0 | 212 .. class:: warningmark |
| 213 | |
| 214 **Note** | |
| 215 | |
| 216 If you are trying to use BLAST RBH matches to identify candidate orthologues | |
| 217 or transfer annotation, you *must* use a percentage identity and minimum | |
| 218 coverage threshold or similiar. See: | |
| 219 | |
| 220 Punta and Ofran (2008) The Rough Guide to In Silico Function Prediction, | |
| 221 or How To Use Sequence and Structure Information To Predict Protein | |
| 222 Function. PLoS Comput Biol 4(10): e1000160. | |
| 223 http://dx.doi.org/10.1371/journal.pcbi.1000160 | |
| 224 | |
| 225 The defaults are to require 70% sequence identity over the aligned region | |
| 226 (using ``pident`` in the BLAST+ tabular output), and that the HSP alignment | |
| 227 covers at least 50% of the query sequence (using ``qcovhsp`` in the BLAST+ | |
| 228 tabular output). | |
| 229 | |
| 230 | |
| 231 **References** | |
| 232 | |
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233 Please cite: |
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234 |
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235 P.J.A. Cock, J.M. Chilton, B. Gruening, J.E. Johnson, N. Soranzo (2015). |
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236 NCBI BLAST+ integrated into Galaxy. |
| 21 | 237 *GigaScience* 4:39 |
| 238 http://dx.doi.org/10.1186/s13742-015-0080-7 | |
| 0 | 239 |
| 240 Christiam Camacho et al. (2009). | |
| 241 BLAST+: architecture and applications. | |
| 21 | 242 *BMC Bioinformatics* 15;10:421. |
| 0 | 243 http://dx.doi.org/10.1186/1471-2105-10-421 |
| 244 | |
| 245 This wrapper is available to install into other Galaxy Instances via the Galaxy | |
| 246 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/blast_rbh | |
| 247 </help> | |
| 10 | 248 <citations> |
| 249 <citation type="doi">10.1186/1471-2105-10-421</citation> | |
| 21 | 250 <citation type="doi">10.1186/s13742-015-0080-7</citation> |
| 10 | 251 </citations> |
| 0 | 252 </tool> |