featurebasedmolecularnetworking-with-openms.md

[eeko-kon]

Update iniFile-GNPSExport.ini to:

<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.6.2" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_6_2.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="GNPSExport" description="Tool to export representative consensus MS/MS scan per consensusElement into a .MGF file format. See the documentation on https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking_with_openms">
    <ITEM name="version" value="2.4.0-develop-2019-02-11" 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;GNPSExport&apos;">
      <ITEM name="in_cm" value="" type="input-file" description="input consensusXML file containing only consensusElements with &apos;peptide&apos; annotations." required="true" advanced="false" supported_formats="*.consensusXML" />
      <ITEMLIST name="in_mzml" type="input-file" description="original mzml files containing the ms2 spectra aka peptide annotation " required="true" advanced="false" supported_formats="*.mzML">
      </ITEMLIST>
      <ITEM name="out" value="" type="output-file" description="Output MGF file" required="true" advanced="false" supported_formats="*.mgf" />
      <ITEM name="output_type" value="merged_spectra" type="string" description="specificity of mgf output information" required="false" advanced="false" restrictions="full_spectra,merged_spectra,most_intense" />
      <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 name="merged_spectra" description="Options for exporting mgf file with merged spectra per consensusElement">
        <ITEM name="cos_similarity" value="0.9" type="double" description="Cosine similarity threshold for merged_spectra output" required="false" advanced="false" />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>

(deleted ms2_bin_size parameter- for the CLI wrappers of the new OpenMS version, the parameter can be given separately from the ini file (error if the parameter is introduced in the ini file) and in this case, does not have to be given at all (default: '0.019999999552965' min: '0.0')

[eeko-kon]

@mwang87

[eeko-kon]

Hey @mwang87 could you update that file when you find time? Just delete the line that has the ms2_bin_size parameter