Mercurial > repos > yating-l > ucsc_blat
view blat.xml @ 0:951076264957 draft
planemo upload commit 9e778f6145837bd749e60913d184d3d90e2677df
author | yating-l |
---|---|
date | Wed, 12 Apr 2017 17:47:43 -0400 |
parents | |
children | eb7fcec3fdba |
line wrap: on
line source
<?xml version="1.0"?> <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0"> <description>Standalone blat sequence search command line tool</description> <requirements> <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ blat #if $noHead == "yes" -noHead #end if -q=$query_type -t=$database_type -mask=$mask '${database}' '${query}' output && sort -k 10,10 -k 12,12n output > '${output_sorted}' ]]></command> <inputs> <param type="data" name="database" format="fasta" /> <param type="data" name="query" format="fasta" /> <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t"> <option value="dna">dna - DNA sequence</option> <option value="prot">prot - protein sequence</option> <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option> </param> <param type="select" name="query_type" format="text" multiple="false" label="query type" help="Choose your query type, the default is rnax" argument="-q"> <option value="dna">dna - DNA sequence </option> <option value="rna">rna - RNA sequence</option> <option value="prot">prot - protein sequence</option> <option value="dnax">dnax - DNA sequence translated in six frames to protein</option> <option value="rnax" selected="true">rnax - DNA sequence translated in three frames to protein</option> </param> <param type="select" name="noHead" format="text" label="Suppresses .psl header (so it's just a tab-separated file)." > <option value="yes" selected="true">Yes, suppresses .psl header</option> <option value="no">No, do not suppresses .psl header</option> </param> <param name="mask" type="select" label="Mask out repeats" help="Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas are ignored entirely in protein or translated searches. Default is lower" argument="-mask"> <option value="lower" selected="true">lower - mask out lower-cased sequence</option> <option value="upper">upper - mask out upper-cased sequence</option> <option value="out">out - mask according to database.out RepeatMasker .out file</option> <option value="file.out">file.out - mask database according to RepeatMasker file.out</option> </param> </inputs> <outputs> <data format="psl" name="output_sorted" label="${tool.name} on ${on_string}"></data> </outputs> <tests> <test> <param name="database" value="amaVit1_Gallus/amaVit1.fa" /> <param name="query" value="amaVit1_Gallus/Gallus_gallus_RefSeq.fa" /> <param name="database_type" value="dnax" /> <param name="query_type" value="rnax" /> <param name="noHead" value="true" /> <param name="mask" value="lower" /> <output name="output_sorted" value="amaVit1_Gallus/amaVit1_Gallus_gallus.psl" /> </test> <test> <param name="database" value="dbia3/dbia3.fa" /> <param name="query" value="dbia3/dmel-all-transcript-r6.13.fasta" /> <param name="database_type" value="dnax" /> <param name="query_type" value="rnax" /> <param name="noHead" value="true" /> <param name="mask" value="lower" /> <output name="output_sorted" value="dbia3/dbia3.sorted.psl" /> </test> </tests> <help> <![CDATA[ BLAT ==== BLAT is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. blat (version: v340)- Standalone blat sequence search command line tool. ------------------------------------------------------------------------- usage: ++++++ $ blat database query [-ooc=11.ooc] output.psl where: database and query are each either a .fa, .nib or .2bit file, or a list of these files with one file name per line. -ooc=11.ooc tells the program to load over-occurring 11-mers from an external file. This will increase the speed by a factor of 40 in many cases, but is not required. output.psl is the name of the output file. documentation: ++++++++++++++ See Blat documentation (http://genome.ucsc.edu/goldenPath/help/blatSpec.html) Source code: ++++++++++++ http://hgdownload.cse.ucsc.edu/admin/exe/ ]]></help> <citations> <citation type="bibtex">@article{kent2002blat, title={BLAT—the BLAST-like alignment tool}, author={Kent, W James}, journal={Genome research}, volume={12}, number={4}, pages={656--664}, year={2002}, publisher={Cold Spring Harbor Lab} }</citation> </citations> </tool>