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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
author galaxyp
date Fri, 08 Apr 2016 15:49:36 -0400
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a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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1 <tool id="msconvert_win" name="msconvert (vendor support)" version="@VERSION@.0">
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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2 <description>Convert and/or filter mass spectrometry files (with vendor support on Windows)</description>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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4 <macros>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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5 <import>msconvert_macros.xml</import>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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6 </macros>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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8 <expand macro="msconvertCommand" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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10 <inputs>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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11 <!-- TODO: add Bruker, Waters, Agilent types -->
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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12 <param format="mzml,mzxml,mz5,mgf,wiff,raw" name="input" type="data" label="Input unrefined MS data" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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14 <expand macro="msconvertInputParameters" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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15 </inputs>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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17 <expand macro="msconvertOutput" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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19 <tests>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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20 <expand macro="msconvert_tests" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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22 <test>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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23 <param name="input" value="small.raw" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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24 <param name="output_type" value="mgf" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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25 <param name="pick_peaks" value="true" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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26 <param name="pick_peaks_algorithm" value="vendor" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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27 <param name="pick_peaks_ms_levels" value="1" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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28 <output name="output" file="small-peakpicking-vendor-ms1.mgf" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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29 </test>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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31 </tests>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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32 <help>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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33 <expand macro="msconvert_help" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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34 </help>
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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35 <expand macro="citations" />
a7be99276cf7 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dc0103e36b921e9bcb86f9e9a402d8e6b4c47345-dirty
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36 </tool>