File: FalseDiscoveryRate_2.ini

package info (click to toggle)
openms 1.11.1-5
  • links: PTS, VCS
  • area: main
  • in suites: jessie, jessie-kfreebsd
  • size: 436,688 kB
  • ctags: 150,907
  • sloc: cpp: 387,126; xml: 71,547; python: 7,764; ansic: 2,626; php: 2,499; sql: 737; ruby: 342; sh: 325; makefile: 128
file content (26 lines) | stat: -rw-r--r-- 3,317 bytes parent folder | download 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
 
<?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="FalseDiscoveryRate" description="Estimates the false discovery rate on peptide and protein level using decoy searches.">
    <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 &apos;1&apos; section for &apos;FalseDiscoveryRate&apos;">
      <ITEM name="in" value="" type="string" description="Identification input file which contains a search against a concatenated sequence database(valid formats: &apos;idXML&apos;)" tags="input file" />
      <ITEM name="fwd_in" value="" type="string" description="Identification input to estimate FDR, forward(valid formats: &apos;idXML&apos;)" tags="input file" />
      <ITEM name="rev_in" value="" type="string" description="Identification input to estimate FDR, decoy run(valid formats: &apos;idXML&apos;)" tags="input file" />
      <ITEM name="out" value="" type="string" description="Identification output with annotated FDR" tags="output file" />
      <ITEM name="proteins_only" value="false" type="string" description="if set, the FDR of the proteins only is calculated" restrictions="true,false" />
      <ITEM name="peptides_only" value="true" type="string" description="if set, the FDR of the peptides only is calculated" restrictions="true,false" />
      <ITEM name="log" value="TOPP.log" type="string" description="Location of the log file" 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" restrictions="true,false" />
      <ITEM name="test" value="false" type="string" description="Enables the test mode (needed for software testing only)" tags="advanced" restrictions="true,false" />
      <NODE name="algorithm" description="Parameter section for the fdr calculation algorithm">
        <ITEM name="q_value" value="true" type="string" description="if &apos;true&apos;, the q-values will be calculated instead of the FDRs" restrictions="true,false" />
        <ITEM name="use_all_hits" value="false" type="string" description="If &apos;true&apos; not only the first hit, but all are used" restrictions="true,false" />
        <ITEM name="split_charge_variants" value="false" type="string" description="If set to &apos;true&apos; charge variants are treated separately (only for combined target/decoy searches)." restrictions="true,false" />
        <ITEM name="treat_runs_separately" value="true" type="string" description="It set to &apos;true&apos; different search runs are treated separately (only for combined target/decoy searches)." restrictions="true,false" />
        <ITEM name="decoy_string" value="_rev" type="string" description="String which is appended at the accession of the protein to indicate that it is a decoy protein." />
      </NODE>
    </NODE>
  </NODE>
</PARAMETERS>