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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="FileConverter" name="FileConverter" version="2.0.0">
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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 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_UID_postprocessing:
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16 -UID_postprocessing
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17 #if " " in str($param_UID_postprocessing):
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18 "$param_UID_postprocessing"
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19 #else
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20 $param_UID_postprocessing
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21 #end if
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22 #end if
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23 #if $param_out:
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24 -out $param_out
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25 #end if
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26 #if $param_out_type:
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27 -out_type
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28 #if " " in str($param_out_type):
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29 "$param_out_type"
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30 #else
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31 $param_out_type
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32 #end if
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33 #end if
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34 #if $param_write_mzML_index:
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35 -write_mzML_index
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36 #end if
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37 -threads \${GALAXY_SLOTS:-24}
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38 #if $adv_opts.adv_opts_selector=='advanced':
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39 #if $adv_opts.param_TIC_DTA2D:
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40 -TIC_DTA2D
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41 #end if
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42 #if $adv_opts.param_MGF_compact:
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43 -MGF_compact
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44 #end if
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45 #if $adv_opts.param_process_lowmemory:
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46 -process_lowmemory
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47 #end if
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48 #if $adv_opts.param_force:
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49 -force
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50 #end if
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51 #end if
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52 </command>
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53 <inputs>
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54 <param name="param_in" type="data" format="mgf,mzml,mzxml,tabular,featurexml,consensusxml" optional="False" label="Input file to convert" help="(-in) "/>
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55 <param name="param_UID_postprocessing" type="select" optional="True" value="ensure" label="unique ID post-processing for output data" help="(-UID_postprocessing) <br>'none' keeps current IDs even if invalid. <br>'ensure' keeps current IDs but reassigns invalid ones. <br>'reassign' assigns new unique IDs">
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56 <option value="none">none</option>
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57 <option value="ensure">ensure</option>
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58 <option value="reassign">reassign</option>
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59 </param>
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60 <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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61 <option value="mzData">mzData</option>
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62 <option value="mzXML">mzXML</option>
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63 <option value="mzML">mzML</option>
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64 <option value="dta2d">dta2d</option>
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65 <option value="mgf">mgf</option>
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66 <option value="featureXML">featureXML</option>
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67 <option value="consensusXML">consensusXML</option>
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68 <option value="edta">edta</option>
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69 <option value="csv">csv</option>
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70 </param>
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71 <param name="param_write_mzML_index" type="boolean" truevalue="-write_mzML_index" falsevalue="" checked="false" optional="True" label="Add an index to the file when writing mzML files (default: no index)" help="(-write_mzML_index) "/>
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72 <expand macro="advanced_options">
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73 <param name="param_TIC_DTA2D" type="boolean" truevalue="-TIC_DTA2D" falsevalue="" 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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74 <param name="param_MGF_compact" type="boolean" truevalue="-MGF_compact" falsevalue="" 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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75 <param name="param_process_lowmemory" type="boolean" truevalue="-process_lowmemory" falsevalue="" 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)" help="(-process_lowmemory) <br>Note: this flag will prevent conversion from spectra to chromatograms"/>
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76 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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77 </expand>
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78 </inputs>
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79 <outputs>
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80 <data name="param_out" metadata_source="param_in" format="input"/>
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81 </outputs>
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82 <help>**What it does**
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83
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84 Converts between different MS file formats.
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85
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86
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87 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html</help>
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88 <expand macro="references"/>
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89 </tool>
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