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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.3" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_3.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="Decharger" description="Decharges and merges different feature charge variants of the same peptide.">
<ITEM name="version" value="1.9.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
<NODE name="1" description="Instance '1' section for 'Decharger'">
<ITEM name="in" value="" type="string" description="input file " tags="input file,required" restrictions="*.FeatureXML" />
<ITEM name="out_cm" value="" type="string" description="output consensus map" tags="output file,required" restrictions="*.ConsensusXML" />
<ITEM name="out_fm" value="" type="string" description="output feature map" tags="output file" restrictions="*.FeatureXML" />
<ITEM name="outpairs" value="" type="string" description="output file" tags="output file" restrictions="*.ConsensusXML" />
<ITEM name="log" value="TOPP.log" type="string" description="Name of log file (created only when specified)" tags="advanced" />
<ITEM name="debug" value="0" type="int" description="Sets the debug level" tags="advanced" />
<ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" />
<ITEM name="no_progress" value="false" type="string" description="Disables progress logging to command line" tags="advanced" restrictions="true,false" />
<ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" tags="advanced" restrictions="true,false" />
<NODE name="algorithm" description="Feature decharging algorithm section">
<NODE name="FeatureDeconvolution" description="">
<ITEM name="charge_min" value="1" type="int" description="Minimal possible charge" />
<ITEM name="charge_max" value="10" type="int" description="Maximal possible charge" />
<ITEM name="charge_span_max" value="4" type="int" description="Maximal range of charges for a single analyte, i.e. observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge" restrictions="1:" />
<ITEM name="q_try" value="feature" type="string" description="Try different values of charge for each feature according to the above settings ('heuristic' [does not test all charges, just the likely ones] or 'all' ), or leave feature charge untouched ('feature')." restrictions="feature,heuristic,all" />
<ITEM name="retention_max_diff" value="1" type="float" description="Maximum allowed RT difference between any two features if their relation shall be determined" />
<ITEM name="retention_max_diff_local" value="1" type="float" description="Maximum allowed RT difference between between two co-features, after adduct shifts have been accounted for (if you do not have any adduct shifts, this value should be equal to 'retention_max_diff', otherwise it should be smaller!)" />
<ITEM name="mass_max_diff" value="0.1" type="float" description="Maximum allowed mass difference [in Th] for a single feature." />
<ITEMLIST name="potential_adducts" type="string" description="Adducts used to explain mass differences in format: 'Element(+)*:Probability[:RTShift[:Label]]', i.e. the number of '+' indicate the charge, e.g. 'Ca++:0.5' indicates +2. Probabilites have to be in (0,1]. RTShift param is optional and indicates the expected RT shift caused by this adduct, e.g. '(2)H4H-4:1:-3' indicates a 4 deuterium label, which causes early elution by 3 seconds. As a fourth parameter you can add a label which is tagged on every feature which has this adduct. This also determines the map number in the consensus file.">
<LISTITEM value="H+:0.7"/>
<LISTITEM value="Na+:0.1"/>
<LISTITEM value="(2)H4H-4:0.1:-2:heavy"/>
</ITEMLIST>
<ITEM name="max_neutrals" value="0" type="int" description="Maximal number of neutral adducts(q=0) allowed. Add them in the 'potential_adducts' section!" />
<ITEM name="max_minority_bound" value="2" type="int" description="Maximum count of the least probable adduct (according to 'potential_adducts' param) within a charge variant. E.g. setting this to 2 will not allow an adduct composition of '1(H+),3(Na+)' if Na+ is the least probable adduct" restrictions="0:" />
<ITEM name="min_rt_overlap" value="0.66" type="float" description="Minimum overlap of the convex hull' RT intersection measured against the union from two features (if CHs are given)" restrictions="0:1" />
<ITEM name="intensity_filter" value="false" type="string" description="Enable the intensity filter, which will only allow edges between two equally charged features if the intensity of the feature with less likely adducts is smaller than that of the other feature. It is not used for features of different charge." restrictions="true,false" />
<ITEM name="default_map_label" value="decharged features" type="string" description="Label of map in output consensus file where all features are put by default" tags="advanced" />
<ITEM name="verbose_level" value="0" type="int" description="Amount of debug information given during processing." tags="advanced" restrictions="0:3" />
</NODE>
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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