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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
author | galaxyp |
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date | Tue, 08 May 2018 14:16:45 -0400 |
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<tool id="BlibSearch" name="BlibSearch" version="@VERSION@.0"> <description>search a spectrum library for matches to query spectra</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ #set $exts = {'mgf':'MGF', 'mzml':'mzML', 'mzxml':'mzXML', 'ms2': 'ms2', 'wiff':'wiff'} #set $ext = $exts[$spectrum_file.extension.lower()] #set $spectrum_name = $spectrum_file.display_name.split('/')[-1].replace($spectrum_file.extension, "") + "." + $ext ln -s -f '${spectrum_file}' '${spectrum_name}' && #set $blib_name = $blib.display_name.split('/')[-1].replace($blib.extension, "") + ".blib" ln -s -f '$blib' '$blib_name' && BlibSearch --clear-precursor $clear_precursor --topPeaksForSearch $topPeaksForSearch --mz-window $mz_window --min-peaks $min_peaks --low-charge $low_charge --high-charge $high_charge --report-matches $report_matches $preserve_order ## --psm-result-file '$psms' --report-file temp.report '$spectrum_name' '$blib_name' && grep -v '^$' temp.report > '$report' ]]></command> <inputs> <param name="spectrum_file" type="data" format="mzml,mzxml,mgf,ms2" label="Spectrum file to search"/> <param name="blib" type="data" format="sqlite" label="Filtered Blib"/> <param name="clear_precursor" type="boolean" value="true" label="Remove the peaks in a X m/z window around the precursor from the query and library spectrum."/> <param name="topPeaksForSearch" type="integer" value="100" label="Use ARG of the highest intensity peaks."/> <param name="mz_window" type="float" value="3" label="Compare query to library spectra with precursor m/z +/- ARG."/> <param name="min_peaks" type="integer" value="20" label="Search only spectra with charge no less than ARG."/> <param name="low_charge" type="integer" value="1" label="Search only spectra with charge no less than ARG."/> <param name="high_charge" type="integer" value="5" label="Search only spectra with charge no higher than ARG."/> <param name="report_matches" type="integer" value="5" label="Return ARG of the best matches for each query. Use -1 to report all."/> <param name="preserve_order" type="boolean" truevalue="--preserve-order" falsevalue="" checked="false" label="Search spectra in the order they appear in the file." help="Default to search as sorted by precursor m/z."/> </inputs> <outputs> <data name="report" format="tabular" label="${spectrum_file.name}.report"> <actions> <action name="comment_lines" type="metadata" default="13" /> <action name="column_names" type="metadata" default="Query,LibId,LibSpec,rank,dotp,query-mz,query-z,lib-mz,lib-z,copies,candidates,sequence,TIC-raw,bp-mz-raw,bp-raw,lbp-mz-raw,num-peaks,matched-ions" /> </actions> </data> <!-- <data name="psms" format="tabular" label="${spectrum_file.name}.psms"/> --> </outputs> <tests> <test> <param name="spectrum_file" ftype="mzml" value="msgf-test.mzML"/> <param name="blib" ftype="sqlite" value="msgf_filterd.blib"/> <output name="report"> <assert_contents> <has_text text="LibSpec" /> <has_text text="VIYTTNAVEAVHRQFRKLTK" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries. BlibSearch_ creates a library of peptide MS/MS spectra from a variety of different database search results. :: Usage: BlibSearch [options] <spectrum-file> <library>[+] Options: -c [ --clear-precursor ] arg (=1) Remove the peaks in a X m/z window around the precursor from the query and library spectrum. --topPeaksForSearch arg (=100) Use ARG of the highest intensity peaks. -w [ --mz-window ] arg (=3) Compare query to library spectra with precursor m/z +/- ARG. -n [ --min-peaks ] arg (=20) Search only spectra with charge no less than ARG. -L [ --low-charge ] arg (=1) Search only spectra with charge no less than ARG. -H [ --high-charge ] arg (=5) Search only spectra with charge no higher than ARG. -m [ --report-matches ] arg (=5) Return ARG of the best matches for each query. Use -1 to report all. --psm-result-file arg Return results in a .psm file named ARG. -R [ --report-file ] arg Return results in report file named ARG. Default is <spectrum file name>.report. --preserve-order Search spectra in the order they appear in the file. Default to search as sorted by precursor m/z. -p [ --parameter-file ] arg File containing search parameters. Command line values override file values. -v [ --verbosity ] arg (=status) Control the level of output to stderr. (silent, error, status, warn, debug, detail, all) Default status. -h [ --help ] Print help message. .. _BlibSearch: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibSearch .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view? ]]></help> <expand macro="citations" /> </tool>