<?xml version='1.0' encoding='UTF-8'?>
<tool id="FidoAdapter" name="FidoAdapter" version="2.0.0">
  <description>Runs the protein inference engine Fido.</description>
  <macros>
    <token name="@EXECUTABLE@">FidoAdapter</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>FidoAdapter
-fidocp_executable FidoChooseParameters
-fido_executable Fido

#if $param_in:
  -in $param_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $param_prob_param:
  -prob_param     "$param_prob_param"
#end if
#if $param_separate_runs:
  -separate_runs
#end if
#if $param_no_cleanup:
  -no_cleanup
#end if
#if $param_all_PSMs:
  -all_PSMs
#end if
#if $param_group_level:
  -group_level
#end if
#if $param_log2_states:
  -log2_states $param_log2_states
#end if
-threads \${GALAXY_SLOTS:-24} 
#if $param_prob_protein:
  -prob:protein $param_prob_protein
#end if
#if $param_prob_peptide:
  -prob:peptide $param_prob_peptide
#end if
#if $param_prob_spurious:
  -prob:spurious $param_prob_spurious
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_keep_zero_group:
  -keep_zero_group
#end if
    #if $adv_opts.param_accuracy:
  -accuracy
  #if " " in str($adv_opts.param_accuracy):
    "$adv_opts.param_accuracy"
  #else
    $adv_opts.param_accuracy
  #end if
#end if
    #if $adv_opts.param_log2_states_precalc:
  -log2_states_precalc $adv_opts.param_log2_states_precalc
#end if
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="idxml" optional="False" label="Input: identification results" help="(-in) "/>
    <param name="param_prob_param" type="text" size="30" value="Posterior Probability_score" label="Read the peptide probability from this user parameter ('UserParam') in the input file, instead of from the 'score' field, if available. (Use" help="(-prob_param) e.g. for search results that were processed with the TOPP tools IDPosteriorErrorProbability followed by FalseDiscoveryRate.)">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_separate_runs" type="boolean" truevalue="-separate_runs" falsevalue="" checked="false" optional="True" label="Process multiple protein identification runs in the input separately, don't merge them" help="(-separate_runs) Merging results in loss of descriptive information of the single protein identification runs"/>
    <param name="param_no_cleanup" type="boolean" truevalue="-no_cleanup" falsevalue="" checked="false" optional="True" label="Omit clean-up of peptide sequences (removal of non-letter characters, replacement of I with L)" help="(-no_cleanup) "/>
    <param name="param_all_PSMs" type="boolean" truevalue="-all_PSMs" falsevalue="" checked="false" optional="True" label="Consider all PSMs of each peptide, instead of only the best one" help="(-all_PSMs) "/>
    <param name="param_group_level" type="boolean" truevalue="-group_level" falsevalue="" checked="false" optional="True" label="Perform inference on protein group level (instead of individual protein level)" help="(-group_level) This will lead to higher probabilities for (bigger) protein groups"/>
    <param name="param_log2_states" type="integer" min="0" optional="True" value="0" label="Binary logarithm of the max" help="(-log2_states) number of connected states in a subgraph. For a value N, subgraphs that are bigger than 2^N will be split up, sacrificing accuracy for runtime. '0' uses the default (18)"/>
    <param name="param_prob_protein" type="float" min="0.0" optional="True" value="0.0" label="Protein prior probability ('gamma' parameter)" help="(-protein) "/>
    <param name="param_prob_peptide" type="float" min="0.0" optional="True" value="0.0" label="Peptide emission probability ('alpha' parameter)" help="(-peptide) "/>
    <param name="param_prob_spurious" type="float" min="0.0" optional="True" value="0.0" label="Spurious peptide identification probability ('beta' parameter)" help="(-spurious) "/>
    <expand macro="advanced_options">
      <param name="param_keep_zero_group" type="boolean" truevalue="-keep_zero_group" falsevalue="" checked="false" optional="True" label="Keep the group of proteins with estimated probability of zero, which is otherwise removed (it may be very large)" help="(-keep_zero_group) "/>
      <param name="param_accuracy" type="select" optional="True" label="Accuracy level of start parameters" help="(-accuracy) There is a trade-off between accuracy and runtime. Empty uses the default ('best')">
        <option value=""></option>
        <option value="best">best</option>
        <option value="relaxed">relaxed</option>
        <option value="sloppy">sloppy</option>
      </param>
      <param name="param_log2_states_precalc" type="integer" min="0" optional="True" value="0" label="Like 'log2_states', but allows to set a separate limit for the precalculation" help="(-log2_states_precalc) "/>
      <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="idxml"/>
  </outputs>
  <help>**What it does**

Runs the protein inference engine Fido.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FidoAdapter.html</help>
  <expand macro="references"/>
</tool>