Mercurial > repos > peterjc > ncbi_blast_plus
view tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml @ 32:b2795652d2b4 draft
Uploaded v0.0.22a, more macros, $GALAXY_SLOTS, more descriptive output names, test makeblastdb
author | peterjc |
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date | Mon, 25 Nov 2013 10:58:46 -0500 |
parents | 5ec998a3530c |
children | 3952ec621ea9 |
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<tool id="ncbi_dustmasker_wrapper" name="NCBI dustmasker" version="0.0.22"> <!-- dustmasker wrapper from Edward Kirton and Nicola Soranzo --> <description>masks low complexity regions</description> <requirements> <requirement type="binary">dustmasker</requirement> <requirement type="package" version="2.2.27">blast+</requirement> </requirements> <version_command>dustmasker -version-full</version_command> <macros> <import>ncbi_macros.xml</import> </macros> <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces dustmasker #if $db_opts.db_opts_selector == "db": -in "${db_opts.database.fields.path}" -infmt blastdb #elif $db_opts.db_opts_selector == "histdb": -in "${os.path.join($db_opts.histdb.extra_files_path, 'blastdb')}" -infmt blastdb #else: -in "$subject" -infmt fasta #end if -out "$outfile" -window $window -level $level -linker $linker -outfmt $outformat </command> <expand macro="stdio" /> <inputs> <expand macro="input_conditional_nucleotide_db" /> <param name="window" type="integer" value="64" label="DUST window length" /> <param name="level" type="integer" value="20" label="DUST level" help="Score threshold for subwindows" /> <param name="linker" type="integer" value="1" label="DUST linker" help="How close masked intervals should be to get merged together" /> <param name="outformat" type="select" label="Output format"> <!-- acclist and maskinfo_xml are listed as possible output formats in "dustmasker -help", but were not recognized by NCBI BLAST up to release 2.2.27+. Fixed in BLAST 2.2.28+. seqloc_* formats are not very useful --> <!-- <option value="acclist">acclist</option>--> <option value="fasta">FASTA</option> <option value="interval" selected="true">interval</option> <option value="maskinfo_asn1_bin">maskinfo ASN.1 binary</option> <option value="maskinfo_asn1_text">maskinfo ASN.1 text</option> <!-- <option value="maskinfo_xml">maskinfo_xml</option> <option value="seqloc_asn1_bin">seqloc_asn1_bin</option> <option value="seqloc_asn1_text">seqloc_asn1_text</option> <option value="seqloc_xml">seqloc_xml</option>--> </param> </inputs> <outputs> <data name="outfile" format="interval" label="DUST Masked File"> <change_format> <when input="outformat" value="fasta" format="fasta" /> <when input="outformat" value="maskinfo_asn1_bin" format="maskinfo-asn1-binary" /> <when input="outformat" value="maskinfo_asn1_text" format="maskinfo-asn1" /> </change_format> </data> </outputs> <tests> <test> <param name="db_opts_selector" value="file" /> <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> <param name="window" value="64" /> <param name="level" value="20" /> <param name="linker" value="1" /> <param name="outformat" value="fasta" /> <output name="outfile" file="dustmasker_three_human.fasta" /> </test> <test> <param name="db_opts_selector" value="file" /> <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> <param name="window" value="64" /> <param name="level" value="20" /> <param name="linker" value="1" /> <param name="outformat" value="maskinfo_asn1_bin" /> <output name="outfile" file="dustmasker_three_human.maskinfo-asn1-binary" /> </test> <test> <param name="db_opts_selector" value="file" /> <param name="subject" value="three_human_mRNA.fasta" ftype="fasta" /> <param name="window" value="64" /> <param name="level" value="20" /> <param name="linker" value="1" /> <param name="outformat" value="maskinfo_asn1_text" /> <output name="outfile" file="dustmasker_three_human.maskinfo-asn1" /> </test> </tests> <help> **What it does** This tool identifies and masks out low complexity regions of a nucleotide database (or sequences in FASTA format) by using the symmetric DUST algorithm. If you select *maskinfo ASN.1* (binary or text) as output format, the output file can be used as masking data for NCBI BLAST+ makeblastdb tool. More information about dustmasker can be found in the `BLAST Command Line Applications User Manual`_. .. _BLAST Command Line Applications User Manual: http://www.ncbi.nlm.nih.gov/books/NBK1763/ **References** If you use this Galaxy tool in work leading to a scientific publication please cite the following papers (a more specific paper covering this wrapper is planned): @REFERENCES@ </help> </tool>