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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="IDMapper" name="IDMapper" version="1.12.0">
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3 <description>Assigns protein/peptide identifications to features or consensus features.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">IDMapper</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>IDMapper
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11
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12 -id ${param_id}
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13 -in ${param_in}
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14 -out ${param_out}
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15 -rt_tolerance ${param_rt_tolerance}
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16 -mz_tolerance ${param_mz_tolerance}
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17 -mz_measure ${param_mz_measure}
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18 -mz_reference ${param_mz_reference}
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19 ${param_ignore_charge}
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20 -threads \${GALAXY_SLOTS:-24}
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21 ${param_use_centroid_rt}
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22 ${param_use_centroid_mz}
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23 ${param_use_subelements}
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24 </command>
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25 <inputs>
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26 <param name="param_id" type="data" format="idXML" optional="False" label="Protein/peptide identifications file" help="(-id)"/>
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27 <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="Feature map/consensus map file" help="(-in)"/>
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28 <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." help="(-rt_tolerance)"/>
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29 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." help="(-mz_tolerance)"/>
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30 <param name="param_mz_measure" type="select" optional="True" value="ppm" label="Unit of 'mz_tolerance'." help="(-mz_measure)">
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31 <option value="ppm">ppm</option>
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32 <option value="Da">Da</option>
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33 </param>
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34 <param name="param_mz_reference" type="select" optional="True" value="precursor" label="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)" help="(-mz_reference)">
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35 <option value="precursor">precursor</option>
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36 <option value="peptide">peptide</option>
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37 </param>
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38 <param name="param_ignore_charge" type="boolean" truevalue="-ignore_charge true" falsevalue="-ignore_charge false" checked="false" optional="True" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature." help="(-ignore_charge)"/>
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39 <param name="param_use_centroid_rt" type="boolean" truevalue="-feature:use_centroid_rt true" falsevalue="-feature:use_centroid_rt false" checked="false" optional="True" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces." help="(-use_centroid_rt)"/>
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40 <param name="param_use_centroid_mz" type="boolean" truevalue="-feature:use_centroid_mz true" falsevalue="-feature:use_centroid_mz false" checked="false" optional="True" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces.#br#(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" help="(-use_centroid_mz)"/>
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41 <param name="param_use_subelements" type="boolean" truevalue="-consensus:use_subelements true" falsevalue="-consensus:use_subelements false" checked="false" optional="True" label="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." help="(-use_subelements)"/>
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42 </inputs>
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43 <outputs>
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44 <data name="param_out" label="Output file (the format depends on the input file format)." format="consensusXML">
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45 <change_format>
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46 <when input="param_out_type" value="featureXML" format="featureXML"/>
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47 </change_format>
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48 </data>
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49 </outputs>
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50 <help>**What it does**
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51
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52 Assigns protein/peptide identifications to features or consensus features.
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53
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54
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55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html
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56
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57 @REFERENCES@
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58 </help>
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59 </tool>
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