Mercurial > repos > galaxyp > bibliospec
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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="BlibFilter" name="BlibFilter" version="@VERSION@.0"> <description>remove redundant spectra from a library</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ BlibFilter --min-peaks $min_peaks --min-score $min_score --best-scoring $best_scoring '$redundant_blib' '$filtered_blib' #if $convert_to_ms2: && BlibToMs2 -f '$ms2' '$filtered_blib' #end if ]]></command> <inputs> <param name="redundant_blib" type="data" format="sqlite" label="Redundant Blib"/> <param name="min_peaks" type="integer" value="1" min="1" label="Only include spectra with at least this peaks" help="--min-peaks"/> <param name="min_score" type="float" value="0" min="0" label="Best spectrum must have at least this average score to be included." help="--min-score"/> <param name="best_scoring" type="boolean" truevalue="1" falsevalue="0" checked="false" label="Use best scoring"/> <param name="convert_to_ms2" type="boolean" truevalue="yes" falsevalue="no" label="Output a MS2"/> </inputs> <outputs> <data name="filtered_blib" format="sqlite" label="Filtered Blib"/> <data name="ms2" format="ms2" label="MS2 from ${on_string}" from_work_dir="spectra.ms2" > <filter>convert_to_ms2 == True</filter> </data> </outputs> <tests> <test> <param name="redundant_blib" ftype="sqlite" value="msgf.blib"/> <param name="convert_to_ms2" value="True"/> <output name="ms2"> <assert_contents> <has_text_matching expression="D\tseq\tFKWNGTDTNSAAEK" /> <has_text_matching expression="D\tmodified seq\tFKWNGTDTNSAAEK" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ BiblioSpec_ is a suite of software tools for creating and searching MS/MS peptide spectrum libraries. BlibFilter_ creates a library of peptide MS/MS spectra from a variety of different database search results. :: Usage: BlibFilter [options] <redundant-library> <filtered-library> Options: -m [ --memory-cache ] arg (=250) SQLite memory cache size in Megs. Default 250M. -n [ --min-peaks ] arg (=1) Only include spectra with at least this many peaks. Default 1. -s [ --min-score ] arg (=0) Best spectrum must have at least this average score to be included. Default 0. -b [ --best-scoring ] arg (=0) Description of option. Default false. -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. .. _BlibFilter: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibFilter .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view? ]]></help> <expand macro="citations" /> </tool>