<tool id="openms_map_aligner_spectrum" version="0.1.0" name="Map Aligner (Spectrum)">
  <description>
    Corrects retention time distortions between maps by aligning spectra.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'MapAlignerSpectrum' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
#set $inputs_as_str = ",".join(map(str, $input))
in=$inputs_as_str
out=@MULTI_OUTPUT($output.extra_files_path,$inputs_as_str)@
#if $generate_transformations
trafo_out=@MULTI_OUTPUT($transformations.extra_files_path,$inputs_as_str)@
#end if
algorithm!gapcost=$gapcost
algorithm!affinegapcost=$affinegapcost
algorithm!scorefunction=$scorefunction
#set $model_type = $model.model_type
model!type=$model_type
#if $model_type == "interpolated"
model!interpolated!interpolation_type=$model.interpolation_type
#end if
</configfile>
  </configfiles>
  <inputs>
    <param format="m:mzml" name="input" type="data" label="Input Peak Lists" />
    <param name="generate_transformations" type="boolean" label="Generate Transformations" />
    <param name="gapcost" type="float" value="1.0" label="Gap Cost" help="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." />
    <param name="affinegapcost" type="float" value="0.5" label="Affine Gap Cost" help="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." />
    <param name="scorefunction" type="select" label="Score Function" help="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.">
      <option value="SteinScottImproveScore">SteinScottImproveScore</option>
      <option value="ZhangSimilarityScore">ZhangSimilarityScore</option>
    </param>
    <expand macro="aligner_model" />
  </inputs>
  <outputs>
    <data format="m:mzml" name="output" label="Alignment of ${on_string}">
    </data>
    <data format="m:trafoxml" name="transformations" label="Aligned Transformations for ${on_string}">
      <filter>generate_transformations</filter>
    </data>
  </outputs>
  <help>
**What it does**

This tool provides an algorithm to align the retention time scales of multiple input files, correcting shifts and distortions between them. Retention time adjustment may be necessary to correct for chromatography differences e.g. before data from multiple LC-MS runs can be combined (feature grouping), or when one run should be annotated with peptide identifications obtained in a different run.

All map alignment tools (MapAligner...) collect retention time data from the input files and - by fitting a model to this data - compute transformations that map all runs to a common retention time scale. They can apply the transformations right away and return output files with aligned time scales (parameter out), and/or return descriptions of the transformations in trafoXML format (parameter trafo_out). Transformations stored as trafoXML can be applied to arbitrary files with the MapRTTransformer tool.

The map alignment tools differ in how they obtain retention time data for the modeling of transformations, and consequently what types of data they can be applied to. Here, an experimental algorithm based on spectrum alignment is implemented. It is only applicable to peak maps (mzML format).

**Citation**

For the underlying tool, please cite ``Weisser et al.: An automated pipeline for high-throughput label-free quantitative proteomics (J. Proteome Res., 2013, PMID: 23391308).``

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
  </help>
</tool>