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annotate FileConverter.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [File Handling]-->
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4 <tool id="FileConverter" name="FileConverter" version="2.0.0">
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5 <description>Converts between different MS file formats.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">FileConverter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>FileConverter
0
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_UID_postprocessing:
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19 -UID_postprocessing
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20 #if &quot; &quot; in str($param_UID_postprocessing):
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21 &quot;$param_UID_postprocessing&quot;
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22 #else
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23 $param_UID_postprocessing
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24 #end if
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25 #end if
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26 #if $param_out:
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27 -out $param_out
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28 #end if
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29 #if $param_out_type:
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30 -out_type
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31 #if &quot; &quot; in str($param_out_type):
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32 &quot;$param_out_type&quot;
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33 #else
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34 $param_out_type
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35 #end if
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36 #end if
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37 #if $param_write_mzML_index:
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38 -write_mzML_index
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39 #end if
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40 -threads \${GALAXY_SLOTS:-24}
0
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41 #if $adv_opts.adv_opts_selector=='advanced':
4
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42 #if $adv_opts.param_TIC_DTA2D:
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43 -TIC_DTA2D
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44 #end if
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45 #if $adv_opts.param_MGF_compact:
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46 -MGF_compact
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47 #end if
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48 #if $adv_opts.param_process_lowmemory:
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49 -process_lowmemory
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50 #end if
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51 #if $adv_opts.param_force:
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52 -force
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53 #end if
0
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54 #end if
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55 </command>
4
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56 <inputs>
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57 <param format="xml,mzml,mzxml,tabular,txt,consensusxml" help="(-in) " label="Input file to convert" name="param_in" optional="False" type="data"/>
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58 <param help="(-UID_postprocessing) &lt;br&gt;'none' keeps current IDs even if invalid. &lt;br&gt;'ensure' keeps current IDs but reassigns invalid ones. &lt;br&gt;'reassign' assigns new unique IDs" label="unique ID post-processing for output data" name="param_UID_postprocessing" optional="True" type="select" value="ensure">
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59 <option value="none">none</option>
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60 <option value="ensure">ensure</option>
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61 <option value="reassign">reassign</option>
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62 </param>
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63 <param help="(-out_type) " label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" name="param_out_type" optional="True" type="select">
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64 <option value="mzData">mzData</option>
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65 <option value="mzXML">mzXML</option>
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66 <option value="mzML">mzML</option>
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67 <option value="dta2d">dta2d</option>
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68 <option value="mgf">mgf</option>
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69 <option value="featureXML">featureXML</option>
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70 <option value="consensusXML">consensusXML</option>
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71 <option value="edta">edta</option>
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72 <option value="csv">csv</option>
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73 </param>
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74 <param checked="false" falsevalue="" help="(-write_mzML_index) " label="Add an index to the file when writing mzML files (default: no index)" name="param_write_mzML_index" optional="True" truevalue="-write_mzML_index" type="boolean"/>
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75 <expand macro="advanced_options">
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76 <param checked="false" falsevalue="" help="(-TIC_DTA2D) " label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" name="param_TIC_DTA2D" optional="True" truevalue="-TIC_DTA2D" type="boolean"/>
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77 <param checked="false" falsevalue="" help="(-MGF_compact) " label="Use a more compact format when writing MGF (no zero-intensity peaks, limited number of decimal places)" name="param_MGF_compact" optional="True" truevalue="-MGF_compact" type="boolean"/>
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78 <param checked="false" falsevalue="" help="(-process_lowmemory) &lt;br&gt;Note: this flag will prevent conversion from spectra to chromatograms" 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)" name="param_process_lowmemory" optional="True" truevalue="-process_lowmemory" type="boolean"/>
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79 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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80 </expand>
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81 </inputs>
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82 <outputs>
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83 <data name="param_out" metadata_source="param_in" format="mgf">
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84 <change_format>
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85 <when input="param_out_type" value="mzData" format="mzData" />
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86 <when input="param_out_type" value="mzXML" format="mzXML" />
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87 <when input="param_out_type" value="mzML" format="mzML" />
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88 <when input="param_out_type" value="dta2d" format="dta2d" />
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89 <when input="param_out_type" value="featureXML" format="featureXML" />
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90 <when input="param_out_type" value="consensusXML" format="consensusXML" />
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91 <when input="param_out_type" value="edta" format="edta" />
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92 <when input="param_out_type" value="csv" format="csv" />
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93 </change_format>
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94 </data>
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95 </outputs>
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96 <help>Converts between different MS file formats.
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97
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98
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99 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_FileConverter.html</help>
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100 </tool>