Mercurial > repos > iuc > mzmine_batch

annotate mzmine_batch.xml @ 0:02e802817d48 draft

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
author iuc
date Sat, 21 Oct 2023 10:29:31 +0000
parents
children 90d60c9da21e
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02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
iuc
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1 <tool id="mzmine_batch" name="MZMine batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
iuc
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2 <macros>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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3 <token name="@TOOL_VERSION@">3.6.0</token>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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4 <token name="@VERSION_SUFFIX@">0</token>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
iuc
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5 </macros>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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6 <xrefs>
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7 <xref type="bio.tools">mzmine</xref>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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8 </xrefs>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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9 <requirements>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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10 <requirement type="package" version="@TOOL_VERSION@">mzmine</requirement>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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11 </requirements>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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12 <command detect_errors="exit_code"><![CDATA[
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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13 #import re
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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14
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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15 mkdir -p input &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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16 #for $i in $input
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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17 #set escaped_i = re.sub('[^\s\w\-\.]', '_', str($i.element_identifier))
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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18 ln -s '$i' 'input/$escaped_i'.$i.ext &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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19 echo 'input/$escaped_i'.$i.ext >> input.txt &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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20 #end for
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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21
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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22 #if $libraries
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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23 mkdir -p libraries &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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24 #for $l in $libraries
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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25 #set escaped_l = re.sub('[^\s\w\-\.]', '_', str($l.element_identifier))
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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26 ln -s '$l' 'libraries/$escaped_l'.$l.ext &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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27 echo 'libraries/$escaped_l'.$l.ext >> libraries.txt &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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28 #end for
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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29 #end if
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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30 ## modify output paths in batch XML to relative path
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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31 ## - any output will be redirected to ./output/BASENAME
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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32 mkdir -p output/ &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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33
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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34 sed -e 's@<current_file>.*[\\\/]\([^\\\/]\+\)</current_file>@<current_file>./output/\1</current_file>@' '$batch' > batch.xml &&
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35
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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36 mzmine
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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37 --batch 'batch.xml'
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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38 --input 'input.txt'
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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39 #if $libraries
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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40 --libraries 'libraries.txt'
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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41 #end if
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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42 --memory "\${MZMINE_MEMORY:-none}"
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43 --temp "\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}"
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44 --threads \${GALAXY_SLOTS:-1}
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45 ## ignored parameters
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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46 ## -p,--pref <arg> preferences file
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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47 ## -r,--running keep MZmine running in headless mode
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48 ## -tdfpseudoprofile Loads pseudo-profile frame spectra for tdf files
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49 ## instead of centroided spectra.
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50 ## -tsfprofile Loads profile spectra from .tsf data instead of
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51 ## centroid spectra.
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52 ]]></command>
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53 <inputs>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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54 <param argument="--batch" type="data" format="xml" label="MZMine batch file" help="XML batch file (ideally created with version @TOOL_VERSION@)"/>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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55 <param argument="--input" type="data" format="mzml,mzxml,csv" multiple="true" label="Spectra (mzml)"/>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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56 <param argument="--libraries" type="data" format="json,mgf,msp" multiple="true" optional="true" label="Spectral libraries"/>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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57 </inputs>
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58 <outputs>
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59 <collection name="output" type="list">
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60 <discover_datasets pattern="__name_and_ext__" directory="output"/>
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61 </collection>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="batch" value="test_small.xml" ftype="xml"/>
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66 <param name="input" value="DOM_a.mzML,DOM_b.mzXML"/>
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67 <param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
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68 <!-- <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_a.mzML"/> -->
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69 <!-- <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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70 <param name="libraries" location="https://external.gnps2.org/gnpslibrary/GNPS-FAULKNERLEGACY.json" ftype="json"/> -->
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71 <output_collection name="output" count="3" type="list">
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72 <element name="test2_iimn_gnps" ftype="mgf">
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73 <assert_contents>
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74 <has_n_lines n="2103"/>
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75 <has_text text="BEGIN IONS"/>
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76 </assert_contents>
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77 </element>
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78 <element name="test2_iimn_gnps_quant" ftype="csv">
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79 <assert_contents>
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80 <has_n_lines n="34"/>
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81 <has_n_columns sep="," n="16"/>
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82 </assert_contents>
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83 </element>
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84 <element name="test2_sirius" ftype="mgf">
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85 <assert_contents>
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86 <has_n_lines n="54406"/>
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87 <has_text text="BEGIN IONS"/>
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88 </assert_contents>
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89 </element>
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90 </output_collection>
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91 </test>
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92 </tests>
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93 <help><![CDATA[
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94 MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data.
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95
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96 This Galaxy tool allows to execute MZmine batches. That is you can create MZmine batch (XML) files thatdescribe the parameters of a MZmine analysis using the MZmine GUI
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97 and use this to execute such an analysis on the Galaxy platform.
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98
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99 **Inputs**
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100
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101 - MZMine batch file in XML format. This file describes the parameters for a MZmine batch analysis. It can be generated with the MZmine GUI (preferentiall with a matching version, i.e. @TOOL_VERSION@).
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102 - Input spectra in mzml format
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103 - Spectra libraries in mgf or json format (optional)
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104
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105 **Outputs**
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106
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107 Galaxy will store all outputs of MZMine in a single collection. When specifying the batch XML
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108 file one should pay attention to use file extensions that correspond to Galaxy datatypes
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109 (which allows Galaxy to easily autodetect the datatype). The following extensions can be used
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110 (lower/upper case does not matter):
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111
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112 - mzml
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113 - netcdf
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114 - mgf
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115 - txt
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116 - msp
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117 - csv
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118 - mztab
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119 - mztab2 (this is mzTab-m)
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120 - json
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121 - tabular (Galaxy's tsv implementation)
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122
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123 Specific datasets from the collection can be accessed using the *Extract dataset* tool, e.g.
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124 for further processing in Galaxy.
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125 ]]></help>
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126 <citations>
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127 <citation type="doi">10.1038/s41587-023-01690-2</citation>
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128 </citations>
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129 </tool>