<?xml version='1.0' encoding='UTF-8'?>
<tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="2.0.0">
  <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
  #for token in $param_in:
    $token
  #end for

#if $rep_param_out:
-out
  #for token in $rep_param_out:
    #if " " in str(token):
      "$token.param_out"
    #else
      $token.param_out
    #end if
  #end for
#end if

#if $rep_param_trafo_out:
-trafo_out
  #for token in $rep_param_trafo_out:
    #if " " in str(token):
      "$token.param_trafo_out"
    #else
      $token.param_trafo_out
    #end if
  #end for
#end if
-threads \${GALAXY_SLOTS:-24} 
#if $param_reference_file:
  -reference:file $param_reference_file
#end if
#if $param_reference_index:
  -reference:index $param_reference_index
#end if
#if $param_algorithm_peptide_score_threshold:
  -algorithm:peptide_score_threshold $param_algorithm_peptide_score_threshold
#end if
#if $param_algorithm_min_run_occur:
  -algorithm:min_run_occur $param_algorithm_min_run_occur
#end if
#if $param_algorithm_max_rt_shift:
  -algorithm:max_rt_shift $param_algorithm_max_rt_shift
#end if
#if $param_algorithm_use_unassigned_peptides:
  -algorithm:use_unassigned_peptides
#end if
#if $param_algorithm_use_feature_rt:
  -algorithm:use_feature_rt
#end if
#if $param_model_type:
  -model:type
  #if " " in str($param_model_type):
    "$param_model_type"
  #else
    $param_model_type
  #end if
#end if
#if $param_model_linear_symmetric_regression:
  -model:linear:symmetric_regression
#end if
#if $param_model_b_spline_wavelength:
  -model:b_spline:wavelength $param_model_b_spline_wavelength
#end if
#if $param_model_b_spline_num_nodes:
  -model:b_spline:num_nodes $param_model_b_spline_num_nodes
#end if
#if $param_model_b_spline_extrapolate:
  -model:b_spline:extrapolate
  #if " " in str($param_model_b_spline_extrapolate):
    "$param_model_b_spline_extrapolate"
  #else
    $param_model_b_spline_extrapolate
  #end if
#end if
#if $param_model_b_spline_boundary_condition:
  -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition
#end if
#if $param_model_interpolated_interpolation_type:
  -model:interpolated:interpolation_type
  #if " " in str($param_model_interpolated_interpolation_type):
    "$param_model_interpolated_interpolation_type"
  #else
    $param_model_interpolated_interpolation_type
  #end if
#end if
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featurexml,consensusxml,idxml" multiple="true" optional="False" size="30" label="Input files separated by blanks (all must have the same file type)" help="(-in) ">
      <sanitizer>
        <valid initial="string.printable">
          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_reference_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_reference_index" type="integer" min="0" optional="True" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="(-index) &lt;br&gt;If '0', no explicit reference is set - the algorithm will select a reference"/>
    <param name="param_algorithm_peptide_score_threshold" type="float" value="0.0" label="Score threshold for peptide hits to be used in the alignment" help="(-peptide_score_threshold) &lt;br&gt;Select a value that allows only 'high confidence' matches"/>
    <param name="param_algorithm_min_run_occur" type="integer" min="2" optional="True" value="2" label="Minimum number of runs (incl" help="(-min_run_occur) reference, if any) a peptide must occur in to be used for the alignment. &lt;br&gt;Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
    <param name="param_algorithm_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" help="(-max_rt_shift) reference). Peptides with higher shifts (outliers) are not used to compute the alignment. &lt;br&gt;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"/>
    <param name="param_algorithm_use_unassigned_peptides" type="boolean" truevalue="-algorithm:use_unassigned_peptides" falsevalue="" checked="true" optional="True" label="Should unassigned peptide identifications be used when computing an alignment of feature maps?" help="(-use_unassigned_peptides) If 'false', only peptide IDs assigned to features will be used"/>
    <param name="param_algorithm_use_feature_rt" type="boolean" truevalue="-algorithm:use_feature_rt" falsevalue="" 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" help="(-use_feature_rt) If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used. &lt;br&gt;Precludes 'use_unassigned_peptides'"/>
    <param name="param_model_type" type="select" optional="True" value="b_spline" 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_model_linear_symmetric_regression" type="boolean" truevalue="-model:linear:symmetric_regression" falsevalue="" checked="false" optional="True" label="Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
    <param name="param_model_b_spline_wavelength" type="float" min="0.0" optional="True" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="(-wavelength) The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
    <param name="param_model_b_spline_num_nodes" type="integer" min="0" optional="True" value="5" label="Number of nodes for B-spline fitting" help="(-num_nodes) Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
    <param name="param_model_b_spline_extrapolate" type="select" optional="True" value="linear" label="Method to use for extrapolation beyond the original data range" help="(-extrapolate) 'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
      <option value="linear">linear</option>
      <option value="b_spline">b_spline</option>
      <option value="constant">constant</option>
      <option value="global_linear">global_linear</option>
    </param>
    <param name="param_model_b_spline_boundary_condition" type="integer" min="0" max="2" optional="True" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help="(-boundary_condition) "/>
    <param name="param_model_interpolated_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_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
    </expand>
  </inputs>
  <outputs>
    <data name="param_out" metadata_source="param_in" format="input"/>
    <data name="param_trafo_out" format="trafoxml"/>
  </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</help>
  <expand macro="references"/>
</tool>