Mercurial > repos > galaxyp > ltq_iquant_cli
view tools/ltq_iquant_cli.xml @ 0:1b8003300cf5 draft default tip
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author | galaxyp |
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date | Fri, 26 Sep 2014 18:46:50 -0400 |
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<tool id="ltq_iquant_cli" name="LTQ-iQuant CLI" version="0.2.0"> <requirements> <requirement type="package" version="22">binaries_for_package_ltq_iquant_cli</requirement> </requirements> <description>Perform quantitation on data labeled with isobaric tags.</description> <command> LTQ-iQuant-cli --report_type ${peptide_report.report_type} --group_type ${group_type} --report ${peptide_report.report} --type ${quant_type} --output $output #if $training.specify --weights ${training.weights} #end if #for $input in $inputs: "${input}" #end for </command> <inputs> <conditional name="peptide_report"> <param name="report_type" type="select" label="Identification Report Type"> <option value="PEPXML">PepXML</option> <option value="SCAFFOLD">Scaffold Spectrum Report</option> <option value="PROTEIN_PILOT">ProteinPilot Peptide Report</option> <option value="MAX_QUANT">MaxQuant MSMS Export</option> </param> <when value="PEPXML"> <param format="pepxml" name="report" type="data" label="Input PepXML"/> </when> <when value="SCAFFOLD"> <param format="text" name="report" type="data" label="Input Scaffold Report"/> </when> <when value="PROTEIN_PILOT"> <param format="text" name="report" type="data" label="Input ProteinPilot Peptide Report"/> </when> <when value="MAX_QUANT"> <param format="text" name="report" type="data" label="Input MaxQuant MSMS Export"/> </when> </conditional> <param name="inputs" multiple="true" type="data" format="mzxml,mzml" label="Peaklist(s)" help=""/> <param name="quant_type" type="select" label="Quantification type"> <option value="FOUR_PLEX">iTRAQ 4-plex</option> <option value="EIGHT_PLEX">iTRAQ 8-plex</option> <option value="TMT_TWO_PLEX">TMT 2-plex</option> <option value="TMT_SIX_PLEX">TMT 6-plex</option> </param> <param name="group_type" type="select" label="Quantify based on grouping of"> <option value="PROTEIN">Proteins</option> <option value="PEPTIDE">Peptides</option> <option value="PEPTIDE_WITH_MODIFICATIONS">Peptides with modifications</option> <option value="PEPTIDE_WITH_UNIQUE_MODIFICATION">Peptide with an identified modification</option> </param> <conditional name="training"> <param name="specify" type="boolean" label="Specify Trained Intensity Weights (Advanced)" checked="false" /> <when value="false"> </when> <when value="true"> <param name="weights" type="data" label="Trained Weights XML File" format="xml" /> </when> </conditional> </inputs> <outputs> <data format="tabular" name="output" /> </outputs> <stdio> <exit_code range="1:" level="fatal" description="Unknown error, exit code non-zero" /> </stdio> <help> **What it does** iQuant is a tool that performs tag based isobaric quantification by implementing a technique assigning collective reporter ion intensity-based weights to each peptide abundance ratio and calculating a protein's weighted average abundance ratio and p-value. iQuant requires identification results from an upstream identification pipeline along with XML peak lists for the data (mzXML is well supported and an mzML option has been provided for testing). ------ **Citation** For the underlying tool, please cite ``Onsongo G, Stone MD, Van Riper SK, Chilton J, Wu B, Higgins L, Lund TC, Carlis JV, Griffin TJ, 2010. LTQ-iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments. Proteomics. 10(19). doi: 10.1002/pmic.201000189.`` If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/iquant </help> </tool>