view IDDecoyProbability.xml @ 0:3d84209d3178 draft

Uploaded

<?xml version='1.0' encoding='UTF-8'?>
<tool id="IDDecoyProbability" name="IDDecoyProbability" version="1.12.0">
  <description>Estimates peptide probabilities using a decoy search strategy.
WARNING: This util is deprecated.</description>
  <macros>
    <token name="@EXECUTABLE@">IDDecoyProbability</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IDDecoyProbability

-in ${param_in}
-fwd_in ${param_fwd_in}
-rev_in ${param_rev_in}
-out ${param_out}
-threads \${GALAXY_SLOTS:-24} 
#if $adv_opts.adv_opts_selector=='advanced':
    -decoy_algorithm:number_of_bins ${adv_opts.param_number_of_bins}
    -decoy_algorithm:lower_score_better_default_value_if_zero ${adv_opts.param_lower_score_better_default_value_if_zero}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="idXML" optional="True" label="Identification input of combined forward decoy search (reindex with PeptideIndexer first)" help="(-in)"/>
    <param name="param_fwd_in" type="data" format="idXML" optional="True" label="Identification input of forward run" help="(-fwd_in)"/>
    <param name="param_rev_in" type="data" format="idXML" optional="True" label="Identification input of decoy run" help="(-rev_in)"/>
    <expand macro="advanced_options">
      <param name="param_number_of_bins" type="integer" value="40" label="Number of bins used for the fitting, if sparse datasets are used, this number should be smaller" help="(-number_of_bins)"/>
      <param name="param_lower_score_better_default_value_if_zero" type="float" value="50.0" label="This value is used if e.g. a E-value score is 0 and cannot be transformed in a real number (log of E-value)" help="(-lower_score_better_default_value_if_zero)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" label="Identification output with forward scores converted to probabilities" format="idXML"/>
  </outputs>
  <help>**What it does**

Estimates peptide probabilities using a decoy search strategy.
WARNING: This util is deprecated.


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

@REFERENCES@
</help>
</tool>