Mercurial > repos > workflow4metabolomics > mzxmlshaper

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
author workflow4metabolomics
date Mon, 07 Oct 2024 11:40:19 +0000
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7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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1 <tool id="mzxmlshaper" name="Mz(X)ML Shaper" version="1.0.0+galaxy0" profile="21.01">
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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2 <description>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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3 conversion into XCMS-supported mz(X)ML file formats
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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4 </description>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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5 <requirements>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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6 <requirement type="package" version="4.3.3">r-base</requirement>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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7 <requirement type="package" version="0.42.0">bioconductor-msdata</requirement>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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8 <requirement type="package" version="2.36.0">bioconductor-mzr</requirement>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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9 <requirement type="package" version="1.0.0">r-w4mrutils</requirement>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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10 </requirements>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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11 <command detect_errors="aggressive"><![CDATA[
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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12 Rscript '$__tool_directory__/mzXMLShaper.R'
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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13 inputfilename '$infile'
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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14 outputfileformat '$outformat'
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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15 #if str($outformat) == 'mzml':
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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16 outputfilename '$mzml_file'
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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17 #elif str($outformat) == 'mzXml':
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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18 outputfilename '$mzXml_file'
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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19 #end if
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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20 ]]></command>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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21 <inputs>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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22 <param name="infile" type="data" format="mzml,mzxml,netcdf" label="File(s) to convert" help="file or collection"/>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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23 <param name="outformat" type="select" label="Desired output format">
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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24 <option value="mzml">mzML</option>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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25 <option value="mzXml">mzXML</option>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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26 </param>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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27 </inputs>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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28 <outputs>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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29 <data format="mzml" label="${infile.name}_converted.mzml" name="mzml_file">
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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30 <filter>outformat=="mzml"</filter>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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31 </data>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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32 <data format="mzxml" label="${infile.name}_converted.mzxml" name="mzXml_file">
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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33 <filter>outformat=="mzXml"</filter>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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34 </data>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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35 </outputs>
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36 <tests>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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37 <test expect_num_outputs="1">
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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38 <param name="infile" value="original_data/ko16.CDF"/>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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39 <param name="outformat" value="mzml"/>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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40 <output name="mzml_file" file="conversion_result_cdf_to_mzml.mzml" />
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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41 </test>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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42 <test expect_num_outputs="1">
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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43 <param name="infile" value="original_data/ko16.CDF"/>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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44 <param name="outformat" value="mzXml"/>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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45 <output name="mzXml_file" file="conversion_result_cdf_to_mzxml.mzxml"/>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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46 </test>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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47 <test expect_num_outputs="1">
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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48 <param name="infile" value="original_data/ko16.mzXml"/>
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49 <param name="outformat" value="mzml"/>
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50 <output name="mzml_file" file="conversion_result_mzxml_to_mzml.mzml" />
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51 </test>
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52 <test expect_num_outputs="1">
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53 <param name="infile" value="original_data/ko16.mzXml"/>
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54 <param name="outformat" value="mzXml"/>
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55 <output name="mzXml_file" file="conversion_result_mzxml_to_mzxml.mzxml"/>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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56 </test>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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57 <test expect_num_outputs="1">
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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58 <param name="infile" value="original_data/ko16.mzml"/>
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59 <param name="outformat" value="mzml"/>
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60 <output name="mzml_file" file="conversion_result_mzml_to_mzml.mzml" />
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61 </test>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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62 <test expect_num_outputs="1">
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63 <param name="infile" value="original_data/ko16.mzml"/>
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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64 <param name="outformat" value="mzXml"/>
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65 <output name="mzXml_file" file="conversion_result_mzml_to_mzxml.mzxml"/>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69 .. class:: infomark
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70
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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71 **Credits**
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72 | **Original tool wrapping:** Quentin Ruin - INRAE - MetaboHUB
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73 | **Tool maintainer:** Mélanie Pétéra - INRAE - MetaboHUB
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74
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75 .. class:: infomark
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76
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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77 **Help and support:** https://community.france-bioinformatique.fr/c/workflow4metabolomics/10
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78
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79 ---------------------------------------------------
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80
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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81 ******************
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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82 Mz(X)ML Shaper
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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83 ******************
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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84 ===========
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85 DESCRIPTION
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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86 ===========
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87
7c20fbf53fbf planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
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88 This tool unables the user to convert any mass spectrometry file from netCDF (.cdf), .mzml or .mzxml format to "Pwiz-style" .mzml or .mzXml, as these are more often supported by the latest software. Files must be standard MS format (see Note below).
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89 It is based on the R package mzR. This package (https://github.com/sneumann/mzR/) allows the user to access, read and copy the content of common MS file formats such as netCDF, mzML and mzXML. The output copy can be made in a different format, thus converting the file.
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90 For more information about this package, see the related documentation (https://bioconductor.org/packages/release/bioc/html/mzR.html)
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91
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92 ---------------------------------------------------
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93
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94 ==========================
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95 ALIGNMENT WITH OTHER TOOLS
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96 ==========================
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97
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98 -----------
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99 INPUT FILES
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100 -----------
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101
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102 Open format MS files (.netCDF, .mzML, .mzXML)
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103
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104 ------------
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105 OUTPUT FILES
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106 ------------
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107
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108 A file (or collection of files) converted in mzML or mzXML with the same name as the input file (except for the extension)
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109
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110 ----------------------------
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111 EXAMPLE OF WORKFLOW POSITION
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112 ----------------------------
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113
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114 Used as first step in any workflow supporting mzML or mzXML formats just before ReadMSData.
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115
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116 ---------------------------------------------------
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117
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118 ===============
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119 TOOL PARAMETERS
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120 ===============
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121
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122 - Desired output format: mzML or MZXML
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123
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124 ---------------------------------------------------
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125
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126 ==================
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127 OUTPUT DESCRIPTION
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128 ==================
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129
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130 Standardized MzML or mzXML files (depending on the user's configuration of the tool)
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131
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132 ---------------------------------------------------
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133
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134 ==============
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135 EXAMPLE OF USE
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136 ==============
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137
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138 .netCDF file upload -> Mz(X)MLShaper -> ReadMSData -> any workflow
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139
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140 ------------
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141 KNOWN ISSUES
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142 ------------
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143
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144 MzR does not read Bruker's DataAnalysis mzML or mzXML files, as they are not "standard" or "Pwiz-style" files (August 2024). This might also be the case for other constructor-converted mzML/mzXML, in that case an "unsupported file format" error will happen. However, this tool is functional for ProteoWizard's MSConvert mzML/mzXML files.
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145
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146 ]]>
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147 </help>
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148 <citations>
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149 <citation type="doi">10.18129/B9.bioc.mzR</citation>
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150 </citations>
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151 </tool>