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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FileConverter" name="FileConverter" version="1.12.0">
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3 <description>Converts between different MS file formats.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">FileConverter</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>FileConverter
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11
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12 -in ${param_in}
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13 -in_type ${param_in_type}
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14 -UID_postprocessing ${param_UID_postprocessing}
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15 -out ${param_out}
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16 -out_type ${param_out_type}
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17 ${param_write_mzML_index}
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18 -threads \${GALAXY_SLOTS:-24}
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19 #if $adv_opts.adv_opts_selector=='advanced':
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20 ${adv_opts.param_TIC_DTA2D}
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21 ${adv_opts.param_MGF_compact}
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22 ${adv_opts.param_process_lowmemory}
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23 #end if
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24 </command>
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25 <inputs>
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26 <param name="param_in" type="data" format="mzXML,mzML,mgf,featureXML,consensusXML" optional="False" label="Input file to convert." help="(-in)"/>
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27 <param name="param_in_type" type="select" optional="True" label="Input file type -- default: determined from file extension or content#br#" help="(-in_type)">
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28 <option value="mzData">mzData</option>
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29 <option value="mzXML">mzXML</option>
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30 <option value="mzML">mzML</option>
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31 <option value="dta">dta</option>
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32 <option value="dta2d">dta2d</option>
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33 <option value="mgf">mgf</option>
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34 <option value="featureXML">featureXML</option>
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35 <option value="consensusXML">consensusXML</option>
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36 <option value="ms2">ms2</option>
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37 <option value="fid">fid</option>
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38 <option value="tsv">tsv</option>
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39 <option value="peplist">peplist</option>
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40 <option value="kroenik">kroenik</option>
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41 <option value="edta">edta</option>
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42 </param>
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43 <param name="param_UID_postprocessing" type="select" optional="True" value="ensure" label="unique ID post-processing for output data.#br#'none' keeps current IDs even if invalid.#br#'ensure' keeps current IDs but reassigns invalid ones.#br#'reassign' assigns new unique IDs." help="(-UID_postprocessing)">
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44 <option value="none">none</option>
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45 <option value="ensure">ensure</option>
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46 <option value="reassign">reassign</option>
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47 </param>
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48 <param name="param_out_type" type="select" optional="True" label="Output file type -- default: determined from file extension or content#br#Note: that not all conversion paths work or make sense." help="(-out_type)">
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49 <option value="mzData">mzData</option>
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50 <option value="mzXML">mzXML</option>
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51 <option value="mzML">mzML</option>
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52 <option value="dta2d">dta2d</option>
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53 <option value="mgf">mgf</option>
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54 <option value="featureXML">featureXML</option>
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55 <option value="consensusXML">consensusXML</option>
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56 <option value="edta">edta</option>
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57 <option value="csv">csv</option>
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58 </param>
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59 <param name="param_write_mzML_index" type="boolean" truevalue="-write_mzML_index true" falsevalue="-write_mzML_index false" checked="false" optional="True" label="Whether to add an index to the file when writing mzML files" help="(-write_mzML_index)"/>
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60 <expand macro="advanced_options">
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61 <param name="param_TIC_DTA2D" type="boolean" truevalue="-TIC_DTA2D true" falsevalue="-TIC_DTA2D false" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -> DTA2D conversions." help="(-TIC_DTA2D)"/>
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62 <param name="param_MGF_compact" type="boolean" truevalue="-MGF_compact true" falsevalue="-MGF_compact false" checked="false" optional="True" label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" help="(-MGF_compact)"/>
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63 <param name="param_process_lowmemory" type="boolean" truevalue="-process_lowmemory true" falsevalue="-process_lowmemory false" checked="false" optional="True" label="Whether to process the file on the fly without loading the whole file into memory first (only for conversions of mzXML/mzML to mzML).#br#Note: this flag will prevent conversion from spectra to chromatograms." help="(-process_lowmemory)"/>
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64 </expand>
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65 </inputs>
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66 <outputs>
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67 <data name="param_out" label="Output file" format="tabular">
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68 <change_format>
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69 <when input="param_out_type" value="mzXML" format="mzXML"/>
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70 <when input="param_out_type" value="mzML" format="mzML"/>
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71 <when input="param_out_type" value="mgf" format="mgf"/>
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72 <when input="param_out_type" value="featureXML" format="featureXML"/>
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73 <when input="param_out_type" value="consensusXML" format="consensusXML"/>
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74 </change_format>
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75 </data>
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76 </outputs>
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77 <help>**What it does**
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78
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79 Converts between different MS file formats.
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80
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81
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82 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html
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83
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84 @REFERENCES@
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85 </help>
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86 </tool>
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