Mercurial > repos > galaxyp > openms_fileconverter

annotate FileConverter.xml @ 10:5ad0b5bf1deb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5-dirty
author galaxyp
date Fri, 17 May 2019 10:11:48 -0400
parents 1a186cc82c8d
children f2388622d581
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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 CTDConverter.-->
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3 <!--Proposed Tool Section: [File Handling]-->
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4 <tool id="FileConverter" name="FileConverter" version="2.3.0">
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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 detect_errors="aggressive"><![CDATA[FileConverter
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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_out:
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19 -out $param_out
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20 #end if
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21 #if $adv_opts.adv_opts_selector=='advanced':
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22 #if $adv_opts.param_UID_postprocessing:
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23 -UID_postprocessing
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24 #if " " in str($adv_opts.param_UID_postprocessing):
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25 "$adv_opts.param_UID_postprocessing"
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26 #else
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27 $adv_opts.param_UID_postprocessing
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28 #end if
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29 #end if
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30 #if $adv_opts.param_out_type:
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31 -out_type
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32 #if " " in str($adv_opts.param_out_type):
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33 "$adv_opts.param_out_type"
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34 #else
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35 $adv_opts.param_out_type
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36 #end if
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37 #end if
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38 #if $adv_opts.param_TIC_DTA2D:
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39 -TIC_DTA2D
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40 #end if
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41 #if $adv_opts.param_MGF_compact:
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42 -MGF_compact
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43 #end if
3
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44 #if $adv_opts.param_force_MaxQuant_compatibility:
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45 -force_MaxQuant_compatibility
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46 #end if
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47 #if $adv_opts.param_force_TPP_compatibility:
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48 -force_TPP_compatibility
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49 #end if
3
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50 #if $adv_opts.param_write_scan_index:
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51 -write_scan_index
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52 #if " " in str($adv_opts.param_write_scan_index):
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53 "$adv_opts.param_write_scan_index"
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54 #else
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55 $adv_opts.param_write_scan_index
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56 #end if
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57 #end if
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58 #if $adv_opts.param_lossy_compression:
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59 -lossy_compression
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60 #end if
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61 #if $adv_opts.param_lossy_mass_accuracy:
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62 -lossy_mass_accuracy $adv_opts.param_lossy_mass_accuracy
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63 #end if
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64 #if $adv_opts.param_process_lowmemory:
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65 -process_lowmemory
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66 #end if
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67 #if $adv_opts.param_force:
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68 -force
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69 #end if
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70 #end if
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71 ]]></command>
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72 <inputs>
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73 <param name="param_in" type="data" format="mzData,mzxml,mzml,cachedMzML,dta,dta2d,mgf,featurexml,consensusxml,ms2,fid,tabular,peplist,kroenik,tabular" optional="False" label="Input file to convert" help="(-in) "/>
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74 <expand macro="advanced_options">
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75 <param name="param_UID_postprocessing" display="radio" type="select" optional="False" value="ensure" label="unique ID post-processing for output data" 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">
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76 <option value="none">none</option>
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77 <option value="ensure" selected="true">ensure</option>
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78 <option value="reassign">reassign</option>
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79 </param>
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80 <param name="param_out_type" type="select" optional="True" label="Output file type -- default: determined from file extension or content &lt;br&gt;Note: that not all conversion paths work or make sense" help="(-out_type) ">
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81 <option value="mzData">mzData</option>
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82 <option value="mzXML">mzXML</option>
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83 <option value="mzML">mzML</option>
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84 <option value="cachedMzML">cachedMzML</option>
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85 <option value="dta2d">dta2d</option>
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86 <option value="mgf">mgf</option>
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87 <option value="featureXML">featureXML</option>
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88 <option value="consensusXML">consensusXML</option>
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89 <option value="edta">edta</option>
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90 <option value="csv">csv</option>
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91 </param>
0
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92 <param name="param_TIC_DTA2D" display="radio" type="boolean" truevalue="-TIC_DTA2D" falsevalue="" checked="false" optional="True" label="Export the TIC instead of the entire experiment in mzML/mzData/mzXML -&gt; DTA2D conversions" help="(-TIC_DTA2D) "/>
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93 <param name="param_MGF_compact" display="radio" 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) "/>
3
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94 <param name="param_force_MaxQuant_compatibility" display="radio" type="boolean" truevalue="-force_MaxQuant_compatibility" falsevalue="" checked="false" optional="True" label="[mzXML output only] Make sure that MaxQuant can read the mzXML and set the msManufacturer to 'Thermo Scientific'" help="(-force_MaxQuant_compatibility) "/>
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95 <param name="param_force_TPP_compatibility" display="radio" type="boolean" truevalue="-force_TPP_compatibility" falsevalue="" checked="false" optional="True" label="[mXML output only] Make sure that TPP parsers can read the mzML and the precursor ion m/z in the file (otherwise it will be set to zero by the TPP)" help="(-force_TPP_compatibility) "/>
3
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96 <param name="param_write_scan_index" display="radio" type="select" optional="False" value="true" label="Append an index when writing mzML or mzXML files" help="(-write_scan_index) Some external tools might rely on it">
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97 <option value="true" selected="true">true</option>
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98 <option value="false">false</option>
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99 </param>
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100 <param name="param_lossy_compression" display="radio" type="boolean" truevalue="-lossy_compression" falsevalue="" checked="false" optional="True" label="Use numpress compression to achieve optimally small file size (attention: may cause small loss of precision; only for mzML data)" help="(-lossy_compression) "/>
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101 <param name="param_lossy_mass_accuracy" type="float" value="-1.0" label="Desired (absolute) m/z accuracy for lossy compression (" help="(-lossy_mass_accuracy) e.g. use 0.0001 for a mass accuracy of 0.2 ppm at 500 m/z, default uses -1.0 for maximal accuracy)"/>
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102 <param name="param_process_lowmemory" display="radio" 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) &lt;br&gt;Note: this flag will prevent conversion from spectra to chromatograms"/>
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103 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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104 </expand>
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105 </inputs>
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106 <outputs>
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107 <data name="param_out" metadata_source="param_in" auto_format="true"/>
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108 </outputs>
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109 <help>Converts between different MS file formats.
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110
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111
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112 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FileConverter.html</help>
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113 </tool>