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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="AdditiveSeries" description="Computes an additive series to quantify a peptide in a set of samples.">
<ITEM name="version" value="1.8.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
<NODE name="1" description="Instance '1' section for 'AdditiveSeries'">
<ITEMLIST name="in" type="string" description="input files separated by blanks (valid formats: 'featureXML')" tags="input file,required">
</ITEMLIST>
<ITEM name="out" value="AdditiveSeries_1_output.tmp" type="string" description="output XML file containg regression line and confidence interval" tags="output file,required" />
<ITEM name="mz_tolerance" value="1" type="float" description="Tolerance in m/z dimension" />
<ITEM name="rt_tolerance" value="50" type="float" description="Tolerance in RT dimension" />
<ITEMLIST name="concentrations" type="float" description="Spiked concentrations" tags="required">
<LISTITEM value="0.236"/>
<LISTITEM value="0.945"/>
<LISTITEM value="1.418"/>
<LISTITEM value="2.836"/>
</ITEMLIST>
<ITEM name="feature_rt" value="1246" type="float" description="RT position of the feature" tags="required" />
<ITEM name="feature_mz" value="675.9" type="float" description="m/z position of the feature" tags="required" />
<ITEM name="standard_rt" value="1246" type="float" description="RT position of the standard" tags="required" />
<ITEM name="standard_mz" value="689.9" type="float" description="m/z position of the standard" tags="required" />
<ITEM name="write_gnuplot_output" value="true" type="string" description="Flag that activates the GNUplot output" restrictions="true,false" />
<ITEM name="out_gp" value="AdditiveSeries_1_gnuplot_tmp" type="string" description="base file name (3 files with different extensions are created)" />
<ITEM name="mz_unit" value="Thomson" type="string" description="the m/z unit of the plot" />
<ITEM name="rt_unit" value="seconds" type="string" description="the RT unit of the plot" />
<ITEM name="log" value="" 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>
</NODE>
</PARAMETERS>
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