Mercurial > repos > galaxyp > flashlfq
view flashlfq.xml @ 1:a30802542619 draft
Uploaded
author | galaxyp |
---|---|
date | Wed, 06 Dec 2017 09:04:50 -0500 |
parents | 8489cc343cde |
children | d042eabcd6ec |
line wrap: on
line source
<tool id="flashlfq" name="FlashLFQ" version="0.1.0"> <description>ultrafast label-free quantification for mass-spectrometry proteomics</description> <requirements> <requirement type="package" version="0.1.99">flashlfq</requirement> </requirements> <command><![CDATA[ FlashLFQ --idt $idt --rep Test2 --ppm $psm --iso $iso #if $intensity == 'integrate': --int true #end if #if $charge == 'precursor': --chg true #end if --pau false ]]></command> <inputs> <param name="idt" type="data" format="tabular" label="identification file"/> <param name="scans" type="data" format="mzml" multiple="true" label="spectrum files"/> <param name="ppm" type="float" value="10" min="1" max="20" label="monoisotopic ppm tolerance"/> <param name="iso" type="float" value="5" min="1" max="10" label="isotopic distribution tolerance in ppm"/> <param name="nis" type="integer" value="2" min="1" max="30" label="number of isotopes required to be observed"/> <param name="intensity" type="select" label="intensity"> <option value="apex" selected="true">use the apex intensity</option> <option value="integrate">integrate chromatographic peak intensity</option> </param> <param name="charge" type="select" label="charge"> <option value="all" selected="true">use all identification detected charge states</option> <option value="precursor">use precursor charge</option> </param> <!-- --> </inputs> <outputs> <data name="log" format="text" label="${tool.name} on ${on_string}: Log" /> <data name="quantifiedBaseSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedBaseSequences.tsv" /> <data name="quantifiedModifiedSequences" format="tabular" label="${tool.name} on ${on_string}: QuantifiedModifiedSequences.tsv" /> <data name="quantifiedPeaks" format="tabular" label="${tool.name} on ${on_string}: QuantifiedPeaks.tsv" /> <data name="quantifiedProteins" format="tabular" label="${tool.name} on ${on_string}: QuantifiedProteins.tsv" /> </outputs> <tests> <test> <param name="idt" value="aggregatePSMs_5ppmAroundZero.psmtsv" ftype="tabular"/> <param name="scans" value="sliced-mzml.mzML" ftype="mzml"/> <param name="ppm" value="12"/> <param name="iso" value="6"/> <output name="log"> <assert_contents> <has_text text="ppmTolerance = 10" /> <has_text text="isotopePpmTolerance = 6" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ **Accepted command-line arguments:** --idt [string | identification file path (TSV format)] --raw [string | MS data file (.raw or .mzML)] --rep [string | repository containing MS data files] --ppm [double | monoisotopic ppm tolerance] (default = 10) --iso [double | isotopic distribution tolerance in ppm] (default = 5) --sil [boolean | silent mode; no console output] (default = false) --pau [boolean | pause at end of run] (default = true) --int [boolean | integrate chromatographic peak intensity instead of using the apex intensity] (default = false) --chg [boolean | use only precursor charge state; when set to false, FlashLFQ looks for all charge states detected in the MS/MS identification file for each peptide] (default = false) --mbr [bool|match between runs] --rmm [bool|require observed monoisotopic mass peak] --nis [int|number of isotopes required to be observed] ]]></help> <citations> <citation type="doi">10.1021/acs.jproteome.7b00608</citation> </citations> </tool>