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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MRMMapper" name="MRMMapper" version="1.12.0">
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3 <description>MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">MRMMapper</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>MRMMapper
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11
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12 -in ${param_in}
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13 -tr ${param_tr}
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14 -out ${param_out}
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15 -precursor_tolerance ${param_precursor_tolerance}
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16 -product_tolerance ${param_product_tolerance}
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17 ${param_no-strict}
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18 -threads \${GALAXY_SLOTS:-24}
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19 </command>
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20 <inputs>
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21 <param name="param_in" type="data" format="mzML" optional="False" label="Input file containing chromatograms (converted mzXML file)" help="(-in)"/>
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22 <param name="param_tr" type="data" format="" optional="False" label="transition file" help="(-tr)"/>
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23 <param name="param_precursor_tolerance" type="float" value="0.1" label="Precursor tolerance when mapping (in Th)" help="(-precursor_tolerance)"/>
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24 <param name="param_product_tolerance" type="float" value="0.1" label="Product tolerance when mapping (in Th)" help="(-product_tolerance)"/>
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25 <param name="param_no-strict" type="boolean" truevalue="-no-strict true" falsevalue="-no-strict false" checked="false" optional="True" label="run in non-strict mode and allow some chromatograms to not be mapped." help="(-no-strict)"/>
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26 </inputs>
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27 <outputs>
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28 <data name="param_out" label="Output file containing mapped chromatograms" format="mzML"/>
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29 </outputs>
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30 <help>**What it does**
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31
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32 MRMMapper maps measured chromatograms (mzML) and the transitions used (TraML)
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33
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34
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35 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MRMMapper.html
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36
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37 @REFERENCES@
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38 </help>
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39 </tool>
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