Mercurial > repos > galaxyp > bibliospec
view BlibBuild.xml @ 0:5a4801b7d106 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/bibliospec commit 68cd288246e3678dc92a179f1f022d30c0f11ce7
author | galaxyp |
---|---|
date | Tue, 08 May 2018 14:16:45 -0400 |
parents | |
children |
line wrap: on
line source
<tool id="BlibBuild" name="BlibBuild" version="@VERSION@.0"> <description>create a library of peptide MS/MS spectra</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ ## Need to symlink to data using name with extension that recognizes #import re #set $exts = {'mgf':'MGF', 'mzml':'mzML', 'mzxml':'mzXML', 'ms2': 'ms2', 'wiff':'wiff'} #for $pl in $peak_lists: #set $dt = $pl.extension #set $bn = $pl.display_name.split('/')[-1] #set $ext = $exts[$dt.lower()] #set $input_name = $re.sub(str(r'(?i)[.]' + $dt),str('.' + $ext), str($bn)) ln -s -f '${pl}' '${input_name}' && #set $encoded_id = $__app__.security.encode_id($pl.id) echo "Spectrum:${pl.display_name}(API:${encoded_id}) " && #end for #set $ext = $identification.extension #set $ident = $identification.display_name.split('/')[-1].replace('.' + str($identification.extension), "") + "." + $ext ln -s -f '$identification' '$ident' && #if $existing_blib: cp '$existing_blib' spectra.blib && #end if BlibBuild #if str($cutoff): -c $cutoff #end if #if $authority: -a $authority #end if #if $library_id: -i $library_id #end if '$ident' spectra.blib && cp spectra.blib $blib #if $convert_to_ms2: && BlibToMs2 -f '$ms2' spectra.blib #end if ]]></command> <inputs> <param name="identification" type="data" format="mzid" label="Peptide Identification Results" > <help> </help> </param> <param name="peak_lists" type="data" format="mzml,mzxml,mgf" multiple="true" optional="true" label="Spectrum Datasets used in the peptide identification"/> <param name="existing_blib" type="data" format="sqlite" label="Add to existing Blib" optional="true"/> <param name="cutoff" type="float" value="" min="0.0" max="1.0" optional="true" label="Specify the cutoff score (0-1)" help=" below which peptide-spectrum matches will be excluded from the library."/> <param name="authority" type="text" value="" optional="true" label="LSID authority. Default proteome.gs.washington.edu"/> <param name="library_id" type="text" value="" optional="true" label="LSID library ID. Default uses file name"/> <param name="convert_to_ms2" type="boolean" truevalue="yes" falsevalue="no" label="Output a MS2"/> </inputs> <outputs> <data name="blib" format="sqlite" label="Blib from ${on_string}" from_work_dir="spectra.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="identification" ftype="mzid" value="msgf-test.mzid"/> <param name="peak_lists" ftype="mzml" value="msgf-test.mzML"/> <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. BlibBuild_ creates a library of peptide MS/MS spectra from a variety of different database search results. :: Usage: BlibBuild [options] <*.blib|*.pep.xml|*.pep.XML|*.pepXML|*.sqt|*.perc.xml|*.dat|*.xtan.xml|*.idpXML|*.group.xml|*.pride.xml|*.msf|*.pdResult|*.mzid|*msms.txt|*final_fragment.csv|*.proxl.xml|*.ssl|*.mlb|*.tsv|*.osw>+ <library_name> -o Overwrite existing library. Default append. -S <filename> Read from file as though it were stdin. -s Result file names from stdin. e.g. ls *sqt | BlibBuild -s new.blib. -u Ignore peptides except those with the unmodified sequences from stdin. -U Ignore peptides except those with the modified sequences from stdin. -H Use more than one decimal place when describing mass modifications. -C <file size> Minimum file size required to use caching for .dat files. Specifiy units as B,K,G or M. Default 800M. -c <cutoff> Score threshold (0-1) for PSMs to be included in library. Higher threshold is more exclusive. -v <level> Level of output to stderr (silent, error, status, warn). Default status. -L Write status and warning messages to log file. -m <size> SQLite memory cache size in Megs. Default 250M. -l <level> ZLib compression level (0-?). Default 3. -i <library_id> LSID library ID. Default uses file name. -a <authority> LSID authority. Default proteome.gs.washington.edu. -x <filename> Specify the path of XML modifications file for parsing MaxQuant files. -P <float> Specify pusher interval for Waters final_fragment.csv files. -d [<filename>] Document the .blib format by writing SQLite commands to a file, or stdout if no filename is given. .. _BlibBuild: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild .. _BiblioSpec: https://skyline.ms/project/home/software/BiblioSpec/begin.view? ]]></help> <expand macro="citations" /> </tool>