annotate IDDecoyProbability.xml @ 2:9f80aaca4a13 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 50c26f7fbe8a2bd1347c860d7a62480865efc254

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Utilities]-->
<tool id="IDDecoyProbability" name="IDDecoyProbability" version="2.1.0">
  <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="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>IDDecoyProbability

#if $param_in:
  -in $param_in
#end if
#if $param_fwd_in:
  -fwd_in $param_fwd_in
#end if
#if $param_rev_in:
  -rev_in $param_rev_in
#end if
#if $param_out:
  -out $param_out
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
    #if $adv_opts.param_decoy_algorithm_number_of_bins:
  -decoy_algorithm:number_of_bins $adv_opts.param_decoy_algorithm_number_of_bins
#end if
    #if $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero:
  -decoy_algorithm:lower_score_better_default_value_if_zero $adv_opts.param_decoy_algorithm_lower_score_better_default_value_if_zero
#end if
#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_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
      <param name="param_decoy_algorithm_number_of_bins" type="integer" value="40" label="Number of bins used for the fitting, if sparse datasets are used, this number should be smalle" help="(-number_of_bins) "/>
      <param name="param_decoy_algorithm_lower_score_better_default_value_if_zero" type="float" value="50.0" label="This value is used if" help="(-lower_score_better_default_value_if_zero) e.g. a E-value score is 0 and cannot be transformed in a real number (log of E-value)"/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" format="idxml"/>
  </outputs>
  <help>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</help>
</tool>