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<?xml version='1.0' encoding='UTF-8'?>
<tool id="MapAlignerSpectrum" name="MapAlignerSpectrum" version="1.12.0">
  <description>Corrects retention time distortions between maps by spectrum alignment.</description>
  <macros>
    <token name="@EXECUTABLE@">MapAlignerSpectrum</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MapAlignerSpectrum

-in ${param_in}
-out ${param_out}
-trafo_out ${param_trafo_out}
-threads \${GALAXY_SLOTS:-24} 
-algorithm:gapcost ${param_gapcost}
-algorithm:affinegapcost ${param_affinegapcost}
-algorithm:scorefunction ${param_scorefunction}
-model:type ${param_type}
${param_symmetric_regression}
-model:interpolated:interpolation_type ${param_interpolation_type}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:cutoff_score ${adv_opts.param_cutoff_score}
    -algorithm:bucketsize ${adv_opts.param_bucketsize}
    -algorithm:anchorpoints ${adv_opts.param_anchorpoints}
    -algorithm:mismatchscore ${adv_opts.param_mismatchscore}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML" optional="False" size="20" label="Input files separated by blanks (all must have the same file type)" help="(-in)"/>
    <param name="param_gapcost" type="float" min="0.0" optional="True" value="1.0" label=" This Parameter stands for the cost of opining a gap in the Alignment. A Gap means that one Spectrum can not be aligned directly to another Spectrum in the Map. This happens, when the similarity of both spectra a too low or even not present. Imagen as a insert or delete of the spectrum in the map. The gap is necessary for aligning, if we open a gap there is a possibility that an another spectrum can be correct aligned with a higher score as before without gap. But to open a gap is a negative event and has to be punished a bit, so such only in case  it 's a good choice to open a gap, if the score is bad enough. The Parameter is to giving as a positive number, the implementation convert it to a negative number." help="(-gapcost)"/>
    <param name="param_affinegapcost" type="float" min="0.0" optional="True" value="0.5" label=" This Parameter controls the cost of extension a already open gap. The idea behind the affine gapcost lies under the assumption, that it is better to get a long distance of connected gaps than to have a structure gap match gap match.  There for the punishment for the extension of a gap has to be lower than the normal gapcost. If the the result of the aligmnet show high compression, it is a good idea to lower the affine gapcost or the normal gapcost." help="(-affinegapcost)"/>
    <param name="param_scorefunction" type="select" optional="True" value="SteinScottImproveScore" label=" The score function is the core of an alignment. The success of an alignment depends mostly of the elected score function. The score function return the similarity of two Spectrum back. The score influence defines later the way of possible traceback. There exist many way of algorithm to calculate the score." help="(-scorefunction)">
      <option value="SteinScottImproveScore">SteinScottImproveScore</option>
      <option value="ZhangSimilarityScore">ZhangSimilarityScore</option>
    </param>
    <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>
    <expand macro="advanced_options">
      <param name="param_cutoff_score" type="float" min="0.0" max="1.0" optional="True" value="0.7" label="The Parameter defines the threshold which filtered Spectra, these Spectra are high potential candidate for deciding the interval of a sub-alignment.  Only those pair of Spectra are selected, which has a score higher or same of the threshold." help="(-cutoff_score)"/>
      <param name="param_bucketsize" type="integer" min="1" optional="True" value="100" label="Defines the numbers of buckets. It is a quantize of the interval of those points, which defines the main alignment(match points). These points have to filtered, to reduce the amount of points for the calculating a smoother spline curve." help="(-bucketsize)"/>
      <param name="param_anchorpoints" type="integer" min="1" max="100" optional="True" value="100" label="Defines the percent of numbers of match points which a selected from one bucket. The high score pairs are previously selected. The reduction of match points helps to get a smoother spline curve." help="(-anchorpoints)"/>
      <param name="param_mismatchscore" type="float" max="0.0" optional="True" value="-5.0" label="Defines the score of two Spectra if they have no similarity to each other. " help="(-mismatchscore)"/>
    </expand>
  </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="mzML"/>
    <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 by spectrum alignment.


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

@REFERENCES@
</help>
</tool>