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<tool id="openms_id_mapper" version="0.1.0" name="ID Mapper">
  <description>
    Assigns protein/peptide identifications to features or consensus features.
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio" />
  <expand macro="requires" />
  <command interpreter="python">
    openms_wrapper.py --executable 'IDMapper' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
id=$id_input
in=$type.map_input
#set $input_type = str($type.input_type)
#if $input_type == "consensusxml"
consensusfeature!use_subelements=$type.use_subelements
#end if
#if $input_type == "featurexml"
feature!use_centroid_rt=$type.use_centroid_rt
feature!use_centroid_mz=$type.use_centroid_mz
#end if
out=$map_output
rt_tolerance=$rt_tolerance
mz_tolerance=$mz_tolerance
mz_measure=$mz_measure
mz_reference=$mz_reference
ignore_charge=$ignore_charge
</configfile>
  </configfiles>
  <inputs>
    <param name="id_input" label="Protein/Peptide Identifications Input" type="data" format="idxml" />
    <conditional name="type">
      <param name="input_type" type="select" label="Map Input Type">
        <option value="consensusxml">Consensus</option>
        <option value="featurexml">Feature</option>
      </param>
      <when value="consensusxml">
        <param format="consensusxml" name="map_input" type="data" label="Input Consensus File"/>
        <param name="use_subelements" label="Use Sub-features" help="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." truevalue="true" falsevalue="false" type="boolean" />
      </when>
      <when value="featurexml">
        <param format="featurexml" name="map_input" type="data" label="Input Feature File"/>
        <param name="use_centroid_rt" label="Use Centroid RT" help="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." truevalue="true" falsevalue="false" type="boolean" />
        <param name="use_centroid_mz" label="Use Centroid m/z" help="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces. (If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" truevalue="true" falsevalue="false" type="boolean" />
      </when>
    </conditional>
    <param name="rt_tolerance" value="5" label="RT Tolerance (seconds)" type="float" />
    <param name="mz_tolerance" value="20" label="m/z Tolerance" type="float" />
    <param name="mz_measure" label="m/z Tolerance Units" type="select">
      <option value="ppm">ppm</option>
      <option value="Da">Da</option>
    </param>
    <param name="mz_reference" label="m/z Reference" type="select" help="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide', masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
      <option value="precursor">precursor</option>
      <option value="peptide">peptide</option>
    </param>
    <param name="ignore_charge" label="Ignore Charge" help="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." truevalue="true" falsevalue="false" type="boolean" />
  </inputs>
  <outputs>
    <data format="consensusxml" name="map_output">
      <change_format>
        <when input="input_type" value="featurexml" format="featurexml" />
      </change_format>
    </data>
  </outputs>
  <help>
**What it does**

The mapping is based on retention times and mass-to-charge values. Roughly, a peptide identification is assigned to a (consensus) feature if its position lies within the boundaries of the feature or close enough to the feature centroid. Peptide identifications that don't match anywhere are still recorded in the resulting map, as "unassigned peptides". Protein identifications are annotated to the whole map, i.e. not to any particular (consensus) feature.

In all cases, tolerance in RT and m/z dimension is applied according to the parameters rt_tolerance and mz_tolerance. Tolerance is understood as "plus or minus x", so the matching range is actually increased by twice the tolerance value.

If several features or consensus features overlap the position of a peptide identification (taking the allowed tolerances into account), the identification is annotated to all of them.

Annotation of feature maps (featureXML input):
If all features have at least one convex hull, peptide positions are matched against the bounding boxes of the convex hulls (of individual mass traces, if available) by default. If not, the positions of the feature centroids are used. The respective coordinates of the centroids are also used for matching (in place of the corresponding ranges from the bounding boxes) if feature:use_centroid_rt or feature:use_centroid_mz are true.

Annotation of consensus maps (consensusXML input):
Peptide positions are always matched against centroid positions. By default, the consensus centroids are used. However, if consensusfeature:use_subelements is set, the centroids of sub-features are considered instead. In this case, a peptide identification is mapped to a consensus feature if any of its sub-features matches.

**Citation**

For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.``

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