view FalseDiscoveryRate.xml @ 3:ec62782f6c68 draft

Uploaded

<?xml version='1.0' encoding='UTF-8'?>
<tool id="FalseDiscoveryRate" name="FalseDiscoveryRate" version="1.12.0">
  <description>Estimates the false discovery rate on peptide and protein level using decoy searches.</description>
  <macros>
    <token name="@EXECUTABLE@">FalseDiscoveryRate</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FalseDiscoveryRate

-in ${param_in}
-fwd_in ${param_fwd_in}
-rev_in ${param_rev_in}
-out ${param_out}
${param_proteins_only}
${param_peptides_only}
-threads \${GALAXY_SLOTS:-24} 
${param_q_value}
${param_use_all_hits}
${param_split_charge_variants}
${param_treat_runs_separately}
-algorithm:decoy_string ${param_decoy_string}
${param_add_decoy_peptides}
</command>
  <inputs>
    <param name="param_in" type="data" format="idXML" optional="True" label="Identification input file which contains a search against a concatenated sequence database. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input." help="(-in)"/>
    <param name="param_fwd_in" type="data" format="idXML" optional="True" label="Identification input to estimate FDR, forward run." help="(-fwd_in)"/>
    <param name="param_rev_in" type="data" format="idXML" optional="True" label="Identification input to estimate FDR, decoy run." help="(-rev_in)"/>
    <param name="param_proteins_only" type="boolean" truevalue="-proteins_only true" falsevalue="-proteins_only false" checked="false" optional="True" label="If set, the FDR of the proteins only is calculated" help="(-proteins_only)"/>
    <param name="param_peptides_only" type="boolean" truevalue="-peptides_only true" falsevalue="-peptides_only false" checked="false" optional="True" label="If set, the FDR of the peptides only is calculated" help="(-peptides_only)"/>
    <param name="param_q_value" type="boolean" truevalue="-algorithm:q_value true" falsevalue="-algorithm:q_value false" checked="true" optional="True" label="If 'true', the q-values will be calculated instead of the FDRs" help="(-q_value)"/>
    <param name="param_use_all_hits" type="boolean" truevalue="-algorithm:use_all_hits true" falsevalue="-algorithm:use_all_hits false" checked="false" optional="True" label="If 'true' not only the first hit, but all are used (peptides only)" help="(-use_all_hits)"/>
    <param name="param_split_charge_variants" type="boolean" truevalue="-algorithm:split_charge_variants true" falsevalue="-algorithm:split_charge_variants false" checked="false" optional="True" label="If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only)." help="(-split_charge_variants)"/>
    <param name="param_treat_runs_separately" type="boolean" truevalue="-algorithm:treat_runs_separately true" falsevalue="-algorithm:treat_runs_separately false" checked="false" optional="True" label="If set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only)." help="(-treat_runs_separately)"/>
    <param name="param_decoy_string" type="text" size="20" value="_rev" label="String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only)." help="(-decoy_string)"/>
    <param name="param_add_decoy_peptides" type="boolean" truevalue="-algorithm:add_decoy_peptides true" falsevalue="-algorithm:add_decoy_peptides false" checked="false" optional="True" label="If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score." help="(-add_decoy_peptides)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Identification output with annotated FDR" format="idXML"/>
  </outputs>
  <help>**What it does**

Estimates the false discovery rate on peptide and protein level using decoy searches.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FalseDiscoveryRate.html

@REFERENCES@
</help>
</tool>