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<?xml version='1.0' encoding='UTF-8'?>
<tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="1.12.0">
  <description>Corrects retention time distortions between maps based on common peptide identifications.</description>
  <macros>
    <token name="@EXECUTABLE@">MapAlignerIdentification</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MapAlignerIdentification

-in ${param_in}
-out ${param_out}
-trafo_out ${param_trafo_out}
-threads \${GALAXY_SLOTS:-24} 
-reference:file ${param_file}
-reference:index ${param_index}
-algorithm:peptide_score_threshold ${param_peptide_score_threshold}
-algorithm:min_run_occur ${param_min_run_occur}
-algorithm:max_rt_shift ${param_max_rt_shift}
${param_use_unassigned_peptides}
${param_use_feature_rt}
-model:type ${param_type}
${param_symmetric_regression}
-model:interpolated:interpolation_type ${param_interpolation_type}
</command>
  <inputs>
    <param name="param_in" type="data" format="featureXML,consensusXML,idXML" optional="False" size="20" label="Input files separated by blanks (all must have the same file type)" help="(-in)"/>
    <param name="param_file" type="data" format="featureXML,consensusXML,idXML" optional="True" label="File to use as reference (same file format as input files required)" help="(-file)"/>
    <param name="param_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.).#br#If '0', no explicit reference is set - the algorithm will select a reference." help="(-index)"/>
    <param name="param_peptide_score_threshold" type="float" value="0.0" label="Score threshold for peptide hits to be used in the alignment.#br#Select a value that allows only 'high confidence' matches." help="(-peptide_score_threshold)"/>
    <param name="param_min_run_occur" type="integer" min="2" optional="True" value="2" label="Minimum number of runs (incl. reference, if any) a peptide must occur in to be used for the alignment.#br#Unless you have very few runs or identifications, increase this value to focus on more informative peptides." help="(-min_run_occur)"/>
    <param name="param_max_rt_shift" type="float" min="0.0" optional="True" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs. reference). Peptides with higher shifts (outliers) are not used to compute the alignment.#br#If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale." help="(-max_rt_shift)"/>
    <param name="param_use_unassigned_peptides" type="boolean" truevalue="-algorithm:use_unassigned_peptides true" falsevalue="-algorithm:use_unassigned_peptides false" checked="true" optional="True" label="Should unassigned peptide identifications be used when computing an alignment of feature maps? If 'false', only peptide IDs assigned to features will be used." help="(-use_unassigned_peptides)"/>
    <param name="param_use_feature_rt" type="boolean" truevalue="-algorithm:use_feature_rt true" falsevalue="-algorithm:use_feature_rt false" checked="false" optional="True" label="When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to. If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.#br#Precludes 'use_unassigned_peptides'." help="(-use_feature_rt)"/>
    <param name="param_type" type="select" optional="True" value="interpolated" label="Type of model" help="(-type)">
      <option value="linear">linear</option>
      <option value="b_spline">b_spline</option>
      <option value="interpolated">interpolated</option>
    </param>
    <param name="param_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression true" falsevalue="-model:linear:symmetric_regression false" checked="false" optional="True" label="Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'." help="(-symmetric_regression)"/>
    <param name="param_interpolation_type" type="select" optional="True" value="cspline" label="Type of interpolation to apply." help="(-interpolation_type)">
      <option value="linear">linear</option>
      <option value="cspline">cspline</option>
      <option value="akima">akima</option>
    </param>
  </inputs>
  <outputs>
    <data name="param_out" label="Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together." format="idXML">
      <change_format>
        <when input="param_out_type" value="featureXML" format="featureXML"/>
        <when input="param_out_type" value="consensusXML" format="consensusXML"/>
      </change_format>
    </data>
    <data name="param_trafo_out" label="Transformation output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together." format="data"/>
  </outputs>
  <help>**What it does**

Corrects retention time distortions between maps based on common peptide identifications.


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

@REFERENCES@
</help>
</tool>