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<?xml version='1.0' encoding='UTF-8'?>
<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="1.12.0">
  <description>Corrects retention time distortions between maps using a pose clustering approach.</description>
  <macros>
    <token name="@EXECUTABLE@">MapAlignerPoseClustering</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MapAlignerPoseClustering

-in ${param_in}
-out ${param_out}
-trafo_out ${param_trafo_out}
-threads \${GALAXY_SLOTS:-24} 
-reference:file ${param_file}
-reference:index ${param_index}
-algorithm:max_num_peaks_considered ${param_max_num_peaks_considered}
-algorithm:superimposer:mz_pair_max_distance ${param_mz_pair_max_distance}
-algorithm:superimposer:num_used_points ${param_num_used_points}
-algorithm:superimposer:scaling_bucket_size ${param_scaling_bucket_size}
-algorithm:superimposer:shift_bucket_size ${param_shift_bucket_size}
-algorithm:pairfinder:second_nearest_gap ${param_second_nearest_gap}
${param_use_identifications}
${param_ignore_charge}
-algorithm:pairfinder:distance_RT:max_difference ${param_max_difference}
-algorithm:pairfinder:distance_MZ:max_difference ${param_max_difference}
-algorithm:pairfinder:distance_MZ:unit ${param_unit}
#if $adv_opts.adv_opts_selector=='advanced':
    -algorithm:superimposer:rt_pair_distance_fraction ${adv_opts.param_rt_pair_distance_fraction}
    -algorithm:superimposer:max_shift ${adv_opts.param_max_shift}
    -algorithm:superimposer:max_scaling ${adv_opts.param_max_scaling}
    -algorithm:superimposer:dump_buckets ${adv_opts.param_dump_buckets}
    -algorithm:superimposer:dump_pairs ${adv_opts.param_dump_pairs}
    -algorithm:pairfinder:distance_RT:exponent ${adv_opts.param_exponent}
    -algorithm:pairfinder:distance_RT:weight ${adv_opts.param_weight}
    -algorithm:pairfinder:distance_MZ:exponent ${adv_opts.param_exponent}
    -algorithm:pairfinder:distance_MZ:weight ${adv_opts.param_weight}
    -algorithm:pairfinder:distance_intensity:exponent ${adv_opts.param_exponent}
    -algorithm:pairfinder:distance_intensity:weight ${adv_opts.param_weight}
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzML,featureXML" 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="mzML,featureXML" 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_max_num_peaks_considered" type="integer" min="-1" optional="True" value="1000" label="The maximal number of peaks/features to be considered per map. To use all, set to '-1'." help="(-max_num_peaks_considered)"/>
    <param name="param_mz_pair_max_distance" type="float" min="0.0" optional="True" value="0.5" label="Maximum of m/z deviation of corresponding elements in different maps.  This condition applies to the pairs considered in hashing." help="(-mz_pair_max_distance)"/>
    <param name="param_num_used_points" type="integer" min="-1" optional="True" value="2000" label="Maximum number of elements considered in each map (selected by intensity).  Use this to reduce the running time and to disregard weak signals during alignment.  For using all points, set this to -1." help="(-num_used_points)"/>
    <param name="param_scaling_bucket_size" type="float" min="0.0" optional="True" value="0.005" label="The scaling of the retention time interval is being hashed into buckets of this size during pose clustering.  A good choice for this would be a bit smaller than the error you would expect from repeated runs." help="(-scaling_bucket_size)"/>
    <param name="param_shift_bucket_size" type="float" min="0.0" optional="True" value="3.0" label="The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering.  A good choice for this would be about the time between consecutive MS scans." help="(-shift_bucket_size)"/>
    <param name="param_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="The distance to the second nearest neighbors must be larger by this factor than the distance to the matching element itself." help="(-second_nearest_gap)"/>
    <param name="param_use_identifications" type="boolean" truevalue="-algorithm:pairfinder:use_identifications true" falsevalue="-algorithm:pairfinder:use_identifications false" checked="false" optional="True" label="Never link features that are annotated with different peptides (only the best hit per peptide identification is taken into account)." help="(-use_identifications)"/>
    <param name="param_ignore_charge" type="boolean" truevalue="-algorithm:pairfinder:ignore_charge true" falsevalue="-algorithm:pairfinder:ignore_charge false" checked="false" optional="True" label="Compare features normally even if their charge states are different" help="(-ignore_charge)"/>
    <param name="param_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Maximum allowed difference in RT in seconds" help="(-max_difference)"/>
    <param name="param_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Maximum allowed difference in m/z (unit defined by 'unit')" help="(-max_difference)"/>
    <param name="param_unit" type="select" optional="True" value="Da" label="Unit of the 'max_difference' parameter" help="(-unit)">
      <option value="Da">Da</option>
      <option value="ppm">ppm</option>
    </param>
    <expand macro="advanced_options">
      <param name="param_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min).  " help="(-rt_pair_distance_fraction)"/>
      <param name="param_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming.  This applies for both directions." help="(-max_shift)"/>
      <param name="param_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming.  The minimal scaling is the reciprocal of this." help="(-max_scaling)"/>
      <param name="param_dump_buckets" type="text" size="20" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to.  A serial number for each invocation will be appended automatically." help="(-dump_buckets)"/>
      <param name="param_dump_pairs" type="text" size="20" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!).  A serial number for each invocation will be appended automatically." help="(-dump_pairs)"/>
      <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
      <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="RT distances are weighted by this factor" help="(-weight)"/>
      <param name="param_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
      <param name="param_weight" type="float" min="0.0" optional="True" value="1.0" label="m/z distances are weighted by this factor" help="(-weight)"/>
      <param name="param_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent)"/>
      <param name="param_weight" type="float" min="0.0" optional="True" value="0.0" label="Distances based on relative intensity are weighted by this factor" help="(-weight)"/>
    </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="featureXML">
      <change_format>
        <when input="param_out_type" value="mzML" format="mzML"/>
      </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 using a pose clustering approach.


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

@REFERENCES@
</help>
</tool>