Mercurial > repos > xuebing > sharplabtool
view tools/metag_tools/blat_wrapper.xml @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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<tool id="blat_wrapper" name="BLAT" version="1.0.0"> <description> compare sequencing reads against UCSC genome builds</description> <command interpreter="python"> #if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off #else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off #end if# ${GALAXY_DATA_INDEX_DIR} </command> <inputs> <conditional name="source"> <param name="source_select" type="select" label="Target source"> <option value="database">Genome Build</option> <option value="input_ref">Your Upload File</option> </param> <when value="database"> <param name="dbkey" type="genomebuild" label="Genome" /> </when> <when value="input_ref"> <param name="input_target" type="data" format="fasta" label="Reference sequence" /> </when> </conditional> <param name="input_query" type="data" format="fasta" label="Sequence file"/> <param name="iden" type="float" size="15" value="90.0" label="Minimal identity (-minIdentity)" /> <param name="tile_size" type="integer" size="15" value="11" label="Minimal size of exact match (-tileSize)" help="Must be between 6 and 18."/> <param name="one_off" type="integer" size="15" value="0" label="Number of mismatch in the word (-oneOff)" help="Must be between 0 and 2." /> </inputs> <outputs> <data name="output1" format="tabular"/> </outputs> <requirements> <requirement type="binary">blat</requirement> </requirements> <tests> <test> <param name="source_select" value="database" /> <param name="dbkey" value="eschColi_K12" /> <param name="input_query" value="blat_wrapper_test1.fa" ftype="fasta"/> <param name="iden" value="90.0" /> <param name="tile_size" value="11" /> <param name="one_off" value="0" /> <output name="output1" file="blat_wrapper_test1.out" /> </test> </tests> <help> .. class:: warningmark Using a smaller word size (*Minimal Size of Exact Match*) will increase the computational time. .. class:: warningmark Using a larger mismatch number (*Number of Mismatch in the Word*) will increase the computational time. ----- **What it does** This tool currently uses the **BLAT** alignment program. Your short reads file is searched against a genome build or another uploaded file. ----- **Example** - Input a multiple fasta file:: >seq1 TGGTAATGGTGGTTTTTTTTTTTTTTTTTTATTTTT - Use the default settings: - alignment identity must be higher than or equal to 90%. - minimal size of exact match to trigger an alignment is 11. - allow 0 mismatches in the above exact match size. - Search against ce2 (C. elegans March 2004), partial result:: 25 1 0 0 0 0 0 0 + seq1 36 10 36 chrI 15080483 9704438 9704464 1 26, 10, 9704438, ggttttttttttttttttttattttt, ggtttttttttttttttttttttttt, 27 0 0 0 0 0 1 32 + seq1 36 9 36 chrI 15080483 1302536 1302595 2 21,6, 9,30, 1302536,1302589, tggtttttttttttttttttt,attttt, tggtttttttttttttttttt,attttt, ----- **Parameters** - *Minimal Identity* (**-minIdentity**) : In percent, the minimum sequence identity between the query and target alignment. Default is 90. - *Minimal Size of Exact Match* (**-tileSize**) : The size of a match that will trigger an alignment. Default is 11. Usually between 8 and 12. Must be between 6 and 18. - *Number of Mismatch in the Word* (**-oneOff**) : The number of mismatches allowed in the word (tile size) and still triggers an alignment. Default is 0. ----- **Reference** **BLAT**: Kent, W James, BLAT--the BLAST-like alignment tool. (2002) Genome Research:12(4) 656-664. </help> </tool>