Mercurial > repos > galaxyp > openms_proteinquantifier
view ProteinQuantifier.xml @ 1:908ae1e4eb28 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author | galaxyp |
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date | Wed, 09 Aug 2017 09:40:10 -0400 |
parents | 7652a9664052 |
children | fbae1b1acf70 |
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<?xml version='1.0' encoding='UTF-8'?> <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> <!--Proposed Tool Section: [Quantitation]--> <tool id="ProteinQuantifier" name="ProteinQuantifier" version="2.2.0"> <description>Compute peptide and protein abundances</description> <macros> <token name="@EXECUTABLE@">ProteinQuantifier</token> <import>macros.xml</import> </macros> <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command>ProteinQuantifier #if $param_in: -in $param_in #end if #if $param_protein_groups: -protein_groups $param_protein_groups #end if #if $param_out: -out $param_out #end if #if $param_peptide_out: -peptide_out $param_peptide_out #end if #if $param_top: -top $param_top #end if #if $param_average: -average #if " " in str($param_average): "$param_average" #else $param_average #end if #end if #if $param_include_all: -include_all #end if #if $param_filter_charge: -filter_charge #end if #if $param_ratios: -ratios #end if #if $param_ratiosSILAC: -ratiosSILAC #end if #if $param_consensus_normalize: -consensus:normalize #end if #if $param_consensus_fix_peptides: -consensus:fix_peptides #end if #if $param_format_separator: -format:separator "$param_format_separator" #end if #if $param_format_quoting: -format:quoting #if " " in str($param_format_quoting): "$param_format_quoting" #else $param_format_quoting #end if #end if #if $param_format_replacement: -format:replacement "$param_format_replacement" #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if #end if </command> <inputs> <param name="param_in" type="data" format="featurexml,consensusxml,idxml" optional="False" label="Input file" help="(-in) "/> <param name="param_protein_groups" type="data" format="idxml" optional="True" label="Protein inference results for the identification runs that were used to annotate the input (" help="(-protein_groups) e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter). <br>Information about indistinguishable proteins will be used for protein quantification"/> <param name="param_top" type="integer" min="0" optional="True" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help="(-top) "/> <param name="param_average" display="radio" type="select" optional="False" value="median" label="Averaging method used to compute protein abundances from peptide abundances" help="(-average) "> <option value="median" selected="true">median</option> <option value="mean">mean</option> <option value="weighted_mean">weighted_mean</option> <option value="sum">sum</option> </param> <param name="param_include_all" display="radio" type="boolean" truevalue="-include_all" falsevalue="" checked="false" optional="True" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help="(-include_all) "/> <param name="param_filter_charge" display="radio" type="boolean" truevalue="-filter_charge" falsevalue="" checked="false" optional="True" label="Distinguish between charge states of a peptide" help="(-filter_charge) For peptides, abundances will be reported separately for each charge; <br>for proteins, abundances will be computed based only on the most prevalent charge of each peptide. <br>By default, abundances are summed over all charge states"/> <param name="param_ratios" display="radio" type="boolean" truevalue="-ratios" falsevalue="" checked="false" optional="True" label="Add the log2 ratios of the abundance values to the output" help="(-ratios) Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) "/> <param name="param_ratiosSILAC" display="radio" type="boolean" truevalue="-ratiosSILAC" falsevalue="" checked="false" optional="True" label="Add the log2 ratios for a triple SILAC experiment to the output" help="(-ratiosSILAC) Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)"/> <param name="param_consensus_normalize" display="radio" type="boolean" truevalue="-consensus:normalize" falsevalue="" checked="false" optional="True" label="Scale peptide abundances so that medians of all samples are equal" help="(-normalize) "/> <param name="param_consensus_fix_peptides" display="radio" type="boolean" truevalue="-consensus:fix_peptides" falsevalue="" checked="false" optional="True" label="Use the same peptides for protein quantification across all samples" help="(-fix_peptides) <br>With 'top 0', all peptides that occur in every sample are considered. <br>Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected, <br>breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/> <param name="param_format_separator" type="text" size="30" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="(-separator) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <param name="param_format_quoting" display="radio" type="select" optional="False" value="double" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, <br>'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) "> <option value="none">none</option> <option value="double" selected="true">double</option> <option value="escape">escape</option> </param> <param name="param_format_replacement" type="text" size="30" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="(-replacement) "> <sanitizer> <valid initial="string.printable"> <remove value="'"/> <remove value="""/> </valid> </sanitizer> </param> <expand macro="advanced_options"> <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> </expand> </inputs> <outputs> <data name="param_out" format="tabular"/> <data name="param_peptide_out" format="tabular"/> </outputs> <help>Compute peptide and protein abundances For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html</help> </tool>