<?xml version="1.0" encoding="UTF-8"?>
<tool version="2.0.0" name="MetaProSIP" docurl="http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MetaProSIP.html" category="Utilities" >
<description><![CDATA[Performs proteinSIP on peptide features for elemental flux analysis.]]></description>
<manual><![CDATA[Performs proteinSIP on peptide features for elemental flux analysis.]]></manual>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="MetaProSIP" description="Performs proteinSIP on peptide features for elemental flux analysis.">
    <ITEM name="version" value="2.0.0" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;MetaProSIP&apos;">
      <ITEM name="in_mzML" value="" type="input-file" description="Centroided MS1 data" required="true" advanced="false" supported_formats="*.mzML" />
      <ITEM name="in_fasta" value="" type="input-file" description="Protein sequence database" required="true" advanced="false" supported_formats="*.fasta" />
      <ITEM name="out_csv" value="" type="output-file" description="Column separated file with feature fitting result." required="true" advanced="false" supported_formats="*.csv" />
      <ITEM name="out_peptide_centric_csv" value="" type="output-file" description="Column separated file with peptide centric result." required="true" advanced="false" supported_formats="*.csv" />
      <ITEM name="in_featureXML" value="" type="input-file" description="Feature data annotated with identifications (IDMapper)" required="true" advanced="false" supported_formats="*.featureXML" />
      <ITEM name="mz_tolerance_ppm" value="10" type="double" description="Tolerance in ppm" required="false" advanced="false" />
      <ITEM name="rt_tolerance_s" value="30" type="double" description="Rolerance window around feature rt for XIC extraction" required="false" advanced="false" />
      <ITEM name="intensity_threshold" value="10" type="double" description="Intensity threshold to collect peaks in the MS1 spectrum." required="false" advanced="false" />
      <ITEM name="correlation_threshold" value="0.7" type="double" description="Correlation threshold for reporting a RIA" required="false" advanced="false" />
      <ITEM name="xic_threshold" value="0.7" type="double" description="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak. If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present." required="false" advanced="false" />
      <ITEM name="decomposition_threshold" value="0.7" type="double" description="Minimum R² of decomposition that must be achieved for a peptide to be reported." required="false" advanced="false" />
      <ITEM name="weight_merge_window" value="5" type="double" description="Decomposition coefficients within +- this rate window will be combined" required="false" advanced="false" />
      <ITEM name="min_correlation_distance_to_averagine" value="-1" type="double" description="Minimum difference in correlation between incorporation pattern and averagine pattern. Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1" required="false" advanced="true" />
      <ITEM name="pattern_15N_TIC_threshold" value="0.95" type="double" description="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account." required="false" advanced="true" />
      <ITEM name="pattern_13C_TIC_threshold" value="0.95" type="double" description="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account." required="false" advanced="true" />
      <ITEM name="heatmap_bins" value="20" type="int" description="Number of RIA bins for heat map generation." required="false" advanced="true" />
      <ITEM name="plot_extension" value="png" type="string" description="Extension used for plots (png|svg|pdf)." required="false" advanced="false" restrictions="png,svg,pdf" />
      <ITEM name="qc_output_directory" value="" type="string" description="Output directory for the quality report" required="false" advanced="false" />
      <ITEM name="use_15N" value="false" type="string" description="Use 15N instead of 13C" required="false" advanced="false" restrictions="true,false" />
      <ITEM name="use_unassigned_ids" value="false" type="string" description="Include identifications not assigned to a feature in pattern detection." required="false" advanced="false" restrictions="true,false" />
      <ITEM name="use_averagine_ids" value="false" type="string" description="Use averagine peptides as model to perform pattern detection on unidentified peptides." required="false" advanced="false" restrictions="true,false" />
      <ITEM name="report_natural_peptides" value="false" type="string" description="Whether purely natural peptides are reported in the quality report." required="false" advanced="false" restrictions="true,false" />
      <ITEM name="filter_monoisotopic" value="false" type="string" description="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" required="false" advanced="false" restrictions="true,false" />
      <ITEM name="cluster" value="false" type="string" description="Perform grouping" required="false" advanced="false" restrictions="true,false" />
      <ITEM name="observed_peak_fraction" value="0.5" type="double" description="Fraction of observed/expected peaks." required="false" advanced="true" />
      <ITEM name="min_consecutive_isotopes" value="2" type="int" description="Minimum number of consecutive isotopic intensities needed." required="false" advanced="true" />
      <ITEM name="score_plot_yaxis_min" value="0" type="double" description="The minimum value of the score axis. Values smaller than zero usually only make sense if the observed peak fraction is set to 0." required="false" advanced="true" />
      <ITEM name="collect_method" value="correlation_maximum" type="string" description="How RIAs are collected." required="false" advanced="true" restrictions="correlation_maximum,decomposition_maximum" />
      <ITEM name="lowRIA_correlation_threshold" value="-1" type="double" description="Correlation threshold for reporting low RIA patterns. Disable and take correlation_threshold value for negative values." 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="string" description="Disables progress logging to command line" required="false" advanced="true" restrictions="true,false" />
      <ITEM name="force" value="false" type="string" description="Overwrite tool specific checks." required="false" advanced="true" restrictions="true,false" />
      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" restrictions="true,false" />
    </NODE>
  </NODE>
</PARAMETERS>
</tool>
