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<?xml version="1.0" encoding="ISO-8859-1"?>
<PARAMETERS version="1.4" xsi:noNamespaceSchemaLocation="http://open-ms.sourceforge.net/schemas/Param_1_4.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<NODE name="InspectAdapter" description="Annotates MS/MS spectra using Inspect.">
<ITEM name="version" value="1.10.0" type="string" description="Version of the tool that generated this parameters file." tags="advanced" />
<NODE name="1" description="Instance '1' section for 'InspectAdapter'">
<ITEM name="in" value="" type="string" description="input file in mzXML or mzData format.#br#Note: In mode 'inspect_out' an Inspect results file is read." tags="input file,required" supported_formats="*.mzXML,*.mzData" />
<ITEM name="out" value="InspectAdapter_1_output.tmp" type="string" description="output file in idXML format.#br#Note: In mode 'inspect_in' an Inspect input file is written." tags="output file,required" supported_formats="*.idXML" />
<ITEM name="inspect_in" value="false" type="string" description="if this flag is set the InspectAdapter will read in mzXML,#br#write an Inspect input file and generate a trie database" restrictions="true,false" />
<ITEM name="inspect_out" value="false" type="string" description="if this flag is set the InspectAdapter will read in a Inspect results file#br#and write idXML" restrictions="true,false" />
<ITEM name="inspect_directory" value="inspect_TEST_directory" type="string" description="the directory in which Inspect is located" />
<ITEM name="temp_data_directory" value="." type="string" description="a directory in which some temporary files can be stored" />
<ITEM name="dbs" value="" type="string" description="name(s) of database(s) to search in (FASTA and SwissProt supported)" />
<ITEM name="trie_dbs" value="" type="string" description="name(s) of databases(s) to search in (trie-format)" />
<ITEM name="new_db" value="Inspect_FASTAFile_test4.tmp" type="string" description="name of the merged trie database" />
<ITEM name="instrument" value="QTOF" type="string" description="the instrument that was used to measure the spectra#br#(If set to QTOF, uses a QTOF-derived fragmentation model,#br#and does not attempt to correct the parent mass.)" restrictions="ESI-ION-TRAP,QTOF,FT-Hybrid" />
<ITEM name="precursor_mass_tolerance" value="1" type="float" description="the precursor mass tolerance" />
<ITEM name="peak_mass_tolerance" value="0.5" type="float" description="the peak mass tolerance" />
<ITEM name="list_modifications" value="false" type="string" description="show a list of the available modifications" restrictions="true,false" />
<ITEM name="modifications" value="10.3+,KRLNH,fix:+16,C:16-,cterm:-16,nterm" type="string" description="the colon-separated modifications; may be#br#<name>,<type>, e.g.: Deamidation,opt or#br#<composition>,<residues>,<type>,<name>, e.g.: H2C2O,KCS,opt,Acetyl or#br#<mass>,<residues>,<type>,<name>, e.g.: 42.0367,KCS,opt,Acetyl or#br#Valid values for type are "fix" and "opt" (default)#br#If you want terminal PTMs, write "cterm" or "nterm" instead of residues" />
<ITEM name="use_monoisotopic_mod_mass" value="false" type="string" description="use monoisotopic masses for the modifications" restrictions="true,false" />
<ITEM name="modifications_xml_file" value="Inspect_PTMs.xml" type="string" description="name of an XML file with the modifications" />
<ITEM name="cleavage" value="Trypsin" type="string" description="the enzyme used for digestion" />
<ITEM name="inspect_output" value="" type="string" description="name for the output file of Inspect (may only be used in a full run)" tags="output file" />
<ITEM name="inspect_input" value="" type="string" description="name for the input file of Inspect (may only be used in a full run)" tags="input file" />
<ITEM name="multicharge" value="true" type="string" description="attempt to guess the precursor charge and mass,#br#and consider multiple charge states if feasible" restrictions="true,false" />
<ITEM name="max_modifications_pp" value="5" type="int" description="number of PTMs permitted in a single peptide." />
<ITEM name="tag_count" value="3" type="int" description="number of tags to generate" />
<ITEM name="no_tmp_dbs" value="false" type="string" description="no temporary databases are used" restrictions="true,false" />
<ITEM name="p_value" value="0.975" type="float" description="annotations with inferior p-value are ignored" />
<ITEM name="contact_name" value="unknown" type="string" description="Name of the contact" />
<ITEM name="contact_institution" value="unknown" type="string" description="Name of the contact institution" />
<ITEM name="contact_info" value="unknown" type="string" description="Some information about the contact" />
<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="blind" description="Options for blind search">
<ITEM name="blind" value="false" type="string" description="perform a blind search (allowing arbitrary modification masses),#br#is preceeded by a normal search to gain a smaller database.#br#(in full mode only)" restrictions="true,false" />
<ITEM name="blind_only" value="false" type="string" description="like blind but no prior search is performed to reduce the database size" restrictions="true,false" />
<ITEM name="p_value_blind" value="1" type="float" description="used for generating the minimized database" />
<ITEM name="min_spp" value="-1" type="int" description="minimum number of spectra a protein has to annotate#br#to be added to the database" />
<ITEM name="snd_db" value="" type="string" description="name of the minimized trie database generated when using blind mode." />
<ITEM name="max_ptm_size" value="250" type="float" description="maximum modification size (in Da) to consider" />
</NODE>
</NODE>
</NODE>
</PARAMETERS>
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