Mercurial > repos > galaxyp > iquant
diff iquant.xml @ 0:44077d92c836 draft
Initial commit.
author | galaxyp |
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date | Thu, 09 May 2013 17:14:17 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/iquant.xml Thu May 09 17:14:17 2013 -0400 @@ -0,0 +1,69 @@ +<tool id="iquant" name="iQuant" version="0.2.0"> + <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 + #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> + </inputs> + + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <requirements> + <requirement type="package" version="1.19.19">tint_proteomics_scripts</requirement><!-- Version 1.19.19 or higher --> + </requirements> + + <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/galaxyp-toolshed-iquant + + </help> +</tool>