Mercurial > repos > galaxyp > openms_idposteriorerrorprobability
diff ctd/ConsensusMapNormalizer.ctd @ 18:6daaa75ccb99 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 6e7368b7f178fbd1f08c28eea1b538add6943a65-dirty"
| author | galaxyp |
|---|---|
| date | Sun, 13 Dec 2020 15:03:50 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctd/ConsensusMapNormalizer.ctd Sun Dec 13 15:03:50 2020 +0000 @@ -0,0 +1,27 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool ctdVersion="1.7" version="2.6.0-pre-exported-20201001" name="ConsensusMapNormalizer" docurl="http://www.openms.de/documentation/TOPP_ConsensusMapNormalizer.html" category="Map Alignment" > +<description><![CDATA[Normalizes maps of one consensusXML file]]></description> +<manual><![CDATA[Normalizes maps of one consensusXML file]]></manual> +<citations> + <citation doi="10.1038/nmeth.3959" url="" /> +</citations> +<PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"> + <NODE name="ConsensusMapNormalizer" description="Normalizes maps of one consensusXML file"> + <ITEM name="version" value="2.6.0-pre-exported-20201001" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" /> + <NODE name="1" description="Instance '1' section for 'ConsensusMapNormalizer'"> + <ITEM name="in" value="" type="input-file" description="input file" required="true" advanced="false" supported_formats="*.consensusXML" /> + <ITEM name="out" value="" type="output-file" description="output file" required="true" advanced="false" supported_formats="*.consensusXML" /> + <ITEM name="algorithm_type" value="robust_regression" type="string" description="The normalization algorithm that is applied. 'robust_regression' scales each map by a fator computed from the ratios of non-differential background features (as determined by the ratio_threshold parameter), 'quantile' performs quantile normalization, 'median' scales all maps to the same median intensity, 'median_shift' shifts the median instead of scaling (WARNING: if you have regular, log-normal MS data, 'median_shift' is probably the wrong choice. Use only if you know what you're doing!)" required="false" advanced="false" restrictions="robust_regression,median,median_shift,quantile" /> + <ITEM name="ratio_threshold" value="0.67" type="double" description="Only for 'robust_regression': the parameter is used to distinguish between non-outliers (ratio_threshold < intensity ratio < 1/ratio_threshold) and outliers." required="false" advanced="false" restrictions="1.0e-03:1.0" /> + <ITEM name="accession_filter" value="" type="string" description="Use only features with accessions (partially) matching this regular expression for computing the normalization factors. Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used." required="false" advanced="true" /> + <ITEM name="description_filter" value="" type="string" description="Use only features with description (partially) matching this regular expression for computing the normalization factors. Useful, e.g., if you have known house keeping proteins in your samples. When this parameter is empty or the regular expression matches the empty string, all features are used (even those without an ID). No effect if quantile normalization is used." required="false" advanced="true" /> + <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" /> + <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" /> + <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" /> + <ITEM name="no_progress" value="false" type="bool" description="Disables progress logging to command line" required="false" advanced="true" /> + <ITEM name="force" value="false" type="bool" description="Overrides tool-specific checks" required="false" advanced="true" /> + <ITEM name="test" value="false" type="bool" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" /> + </NODE> + </NODE> +</PARAMETERS> +</tool>