Mercurial > repos > devteam > ncbi_blast_plus
view tools/ncbi_blast_plus/ncbi_makeprofiledb.xml @ 26:2889433c7ae1 draft
v0.3.3 - fixed legacy dependecy definition
author | peterjc |
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date | Sat, 20 Jul 2019 18:36:36 -0400 |
parents | e25d3acf6e68 |
children | 6f8ea4b9a2c4 |
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<tool id="ncbi_makeprofiledb" name="NCBI BLAST+ makeprofiledb" version="@WRAPPER_VERSION@"> <description>Make profile database</description> <macros> <token name="@BINARY@">makeprofiledb</token> <import>ncbi_macros.xml</import> </macros> <expand macro="preamble" /> <command detect_errors="aggressive" strict="true"> ##Unlike makeblastdb, makeprofiledb needs directory to exist already: mkdir -p $outfile.files_path && makeprofiledb -out '${os.path.join($outfile.files_path, "blastdb")}' ##We turn $input_file into $infiles with a configfile entry defined below -in '$infiles' #if $title: -title '$title' #else: ##Would default to being based on the cryptic Galaxy filenames, which is unhelpful -title 'Profile Database' #end if -threshold $threshold #if str($contain_pssm_scores.contain_pssm_scores_type) == 'no': -gapopen $contain_pssm_scores.gapopen -gapextend $contain_pssm_scores.gapextend -scale $contain_pssm_scores.scale -matrix $contain_pssm_scores.matrix #end if -obsr_threshold $obsr_threshold -exclude_invalid $exclude_invalid -logfile '$outfile' </command> <configfiles> <configfile name="infiles"> #for $infile in $input_file ${infile} #end for </configfile> </configfiles> <inputs> <param name="input_file" argument="-in" type="data" multiple="true" optional="false" format="pssm-asn1" label="Input PSSM files(s)" help="One or NCBI PSSM ASN.1 format scoremat files (often named *.smp)" /> <param argument="-title" type="text" value="" label="Title for the profile database" help="This is the database name shown in BLAST search output" /> <param argument="-threshold" type="float" size="5" value="9.82" label="Minimum word score to add a word to the lookup table" /> <!-- output options --> <!-- Initially we're only offering the default, RPS databases for use with rpsblast and rpstblastn <param name="dbtype" type="select" display="radio" label="Type of database"> <option value="cobalt">Cobalt</option> <option value="delta">Delta</option> <option value="rps" selected="true">RPS</option> </param> --> <conditional name="contain_pssm_scores"> <param name="contain_pssm_scores_type" type="select" label="Does your input file contain PSSM scores?"> <option value="yes" selected="true">Yes</option> <option value="no">No</option> </param> <when value="yes" /> <when value="no"> <param argument="-gapopen" type="integer" size="5" value="" label="Cost to open a gap" /> <param argument="-gapextend" type="integer" size="5" value="" label="Cost to extend a gap" /> <param argument="-scale" type="float" size="5" value="" label="PSSM scale factor" /> <expand macro="input_scoring_matrix" /> </when> </conditional> <!-- Delta Blast Options --> <param argument="-exclude_invalid" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Exclude invalid domains?" help="Exclude domains that do not pass validation test" /> <param argument="-obsr_threshold" type="float" size="5" value="6.0" label="Observation threshold" help="Exclude domains with with maximum number of independent observations below this threshold" /> </inputs> <outputs> <data name="outfile" format="blastdbd" label="RPS database from ${on_string}" /> </outputs> <tests> <test> <param name="input_file" value="cd00003.smp,cd00008.smp" ftype="pssm-asn1" /> <param name="title" value="Just 2 PSSM matrices" /> <param name="contain_pssm_scores_type" value="yes" /> <output name="outfile" file="empty_file.dat" ftype="blastdbd" > <extra_files type="file" value="cd00003_and_cd00008.phr" name="blastdb.phr" /> <extra_files type="file" value="cd00003_and_cd00008.pin" name="blastdb.pin" compare="sim_size" delta="8" /> <extra_files type="file" value="cd00003_and_cd00008.psq" name="blastdb.psq" /> <extra_files type="file" value="cd00003_and_cd00008.freq" name="blastdb.freq" /> <extra_files type="file" value="cd00003_and_cd00008.loo" name="blastdb.loo" /> <extra_files type="file" value="cd00003_and_cd00008.psd" name="blastdb.psd" /> <extra_files type="file" value="cd00003_and_cd00008.psi" name="blastdb.psi" /> <extra_files type="file" value="cd00003_and_cd00008.rps" name="blastdb.rps" /> <extra_files type="file" value="cd00003_and_cd00008.aux" name="blastdb.aux" /> </output> </test> </tests> <help> **What it does** Make a protein domain profile database (for use with RPS-BLAST or RSP-TBLASTN) from one or more Position Specific Scoring Matrices (PSSM) files in the NCBI "scoremat" ASN.1 format (usually named ``*.smp``). This is a wrapper for the NCBI BLAST+ tool 'makeprofiledb'. More information about makeprofiledb can be found in the `BLAST Command Line Applications User Manual`_. .. _BLAST Command Line Applications User Manual: https://www.ncbi.nlm.nih.gov/books/NBK279690/ **References** If you use this Galaxy tool in work leading to a scientific publication please cite the following papers: @REFERENCES@ </help> <expand macro="blast_citations" /> </tool>