Mercurial > repos > iuc > mzmine_batch

annotate mzmine_batch.xml @ 1:90d60c9da21e draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
author iuc
date Fri, 10 Nov 2023 14:20:45 +0000
parents 02e802817d48
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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
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2 <macros>
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3 <token name="@TOOL_VERSION@">3.9.0</token>
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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
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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>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">mzmine</requirement>
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90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
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11 <requirement type="package" version="3.11">python</requirement>
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12 </requirements>
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13 <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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14 #import re
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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15
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16 mkdir -p input &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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17 #for $i in $input
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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18 #set escaped_i = re.sub('[^\s\w\-\.]', '_', str($i.element_identifier))
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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19 ln -s '$i' 'input/$escaped_i'.$i.ext &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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20 echo 'input/$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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21 #end for
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22
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23 #if $libraries
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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24 mkdir -p libraries &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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25 #for $l in $libraries
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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26 #set escaped_l = re.sub('[^\s\w\-\.]', '_', str($l.element_identifier))
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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27 ln -s '$l' 'libraries/$escaped_l'.$l.ext &&
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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28 echo 'libraries/$escaped_l'.$l.ext >> libraries.txt &&
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29 #end for
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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30 #end if
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31 ## modify output paths in batch XML to relative path
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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32 ## - any output will be redirected to ./output/BASENAME
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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33 mkdir -p output/ &&
1
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34 python '$__tool_directory__/set_path.py'
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
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35 --input '$batch'
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
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36 --output batch.xml
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
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37 #if $localdb
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
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38 --localdb '$localdb'
90d60c9da21e planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit 889d26f1e96edf1f2608ce0dba2d66e8ee60e313
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39 #end if
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40 &&
0
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41
1
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42 ## https://github.com/mzmine/mzmine3/issues/1534
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43 JAVA_OPTS="-XX:ActiveProcessorCount=\${GALAXY_SLOTS:-1}"
0
02e802817d48 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/blob/master/tools/mzmine/ commit dbad3fc09e109598befcec3a9a000496f4e0c9dd
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44 mzmine
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45 --batch 'batch.xml'
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46 --input 'input.txt'
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47 #if $libraries
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48 --libraries 'libraries.txt'
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49 #end if
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50 --memory "\${MZMINE_MEMORY:-none}"
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51 --temp "\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}"
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52 --threads \${GALAXY_SLOTS:-1}
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53 ## ignored parameters
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54 ## -p,--pref <arg> preferences file
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55 ## -r,--running keep MZmine running in headless mode
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56 ## -tdfpseudoprofile Loads pseudo-profile frame spectra for tdf files
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57 ## instead of centroided spectra.
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58 ## -tsfprofile Loads profile spectra from .tsf data instead of
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59 ## centroid spectra.
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60 ]]></command>
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61 <inputs>
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62 <param argument="--batch" type="data" format="xml" label="MZMine batch file" help="XML batch file (ideally created with version @TOOL_VERSION@)"/>
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63 <param argument="--input" type="data" format="mzml,mzxml,csv" multiple="true" label="Spectra (mzml)"/>
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64 <param argument="--libraries" type="data" format="json,mgf,msp" multiple="true" optional="true" label="Spectral libraries"/>
1
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65 <param name="localdb" type="data" format="csv,tsv,tabular,txt" optional="true" label="Local database" help="For 'Custom database search'"/>
0
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66 </inputs>
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67 <outputs>
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68 <collection name="output" type="list">
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69 <discover_datasets pattern="__name_and_ext__" directory="output"/>
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70 </collection>
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71 </outputs>
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72 <tests>
1
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73 <!-- <test>
0
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74 <param name="batch" value="test_small.xml" ftype="xml"/>
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75 <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
0
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76 <param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
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77 <output_collection name="output" count="3" type="list">
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78 <element name="test2_iimn_gnps" ftype="mgf">
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79 <assert_contents>
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80 <has_n_lines n="2103"/>
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81 <has_text text="BEGIN IONS"/>
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82 </assert_contents>
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83 </element>
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84 <element name="test2_iimn_gnps_quant" ftype="csv">
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85 <assert_contents>
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86 <has_n_lines n="34"/>
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87 <has_n_columns sep="," n="16"/>
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88 </assert_contents>
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89 </element>
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90 <element name="test2_sirius" ftype="mgf">
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91 <assert_contents>
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92 <has_n_lines n="54406"/>
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93 <has_text text="BEGIN IONS"/>
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94 </assert_contents>
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95 </element>
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96 </output_collection>
1
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97 <assert_stderr>
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98 <has_text text="INFO: Starting processing of task Local CSV identification using database" negate="true"/>
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99 <has_text text="INFO: Finished a batch of 11 steps"/>
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100 </assert_stderr>
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101 </test> -->
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102 <!-- test with localdb -->
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103 <!-- <test>
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104 <param name="batch" value="test_localdatabase.xml" ftype="xml"/>
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105 <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
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106 <param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
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107 <param name="localdb" value="local_database.csv" ftype="csv"/>
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108 <output_collection name="output" count="3" type="list">
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109 <element name="test2_iimn_gnps" ftype="mgf">
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110 <assert_contents>
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111 <has_n_lines n="2103"/>
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112 <has_text text="BEGIN IONS"/>
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113 </assert_contents>
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114 </element>
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115 <element name="test2_iimn_gnps_quant" ftype="csv">
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116 <assert_contents>
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117 <has_n_lines n="34"/>
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118 <has_n_columns sep="," n="16"/>
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119 </assert_contents>
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120 </element>
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121 <element name="test2_sirius" ftype="mgf">
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122 <assert_contents>
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123 <has_n_lines n="54406"/>
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124 <has_text text="BEGIN IONS"/>
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125 </assert_contents>
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126 </element>
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127 </output_collection>
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128 <assert_stderr>
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129 <has_text text="INFO: Starting processing of task Local CSV identification using database"/>
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130 <has_text text="INFO: Finished a batch of 12 steps"/>
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131 </assert_stderr>
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132 </test> -->
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133 <!-- test with localdb in batch, but user does not provide one-->
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134 <!-- <test expect_failure="true" expect_exit_code="1">
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135 <param name="batch" value="test_localdatabase.xml" ftype="xml"/>
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136 <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_a.mzML,https://raw.githubusercontent.com/mzmine/mzmine3/v@TOOL_VERSION@/src/test/resources/rawdatafiles/DOM_b.mzXML"/>
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137 <param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
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138 <assert_stderr>
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139 <has_text text="Batch file contains LocalCSVDatabaseSearchModule but no local DB CSV file given"/>
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140 </assert_stderr>
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141 </test> -->
0
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142 </tests>
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143 <help><![CDATA[
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144 MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data.
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145
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146 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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147 and use this to execute such an analysis on the Galaxy platform.
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148
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149 **Inputs**
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150
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151 - 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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152 - Input spectra in mzml format
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153 - Spectra libraries in mgf or json format (optional)
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154
1
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155 If the batch file contains steps requiring input data sets these need to be provided
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156 via the optional inputs. Currently this is:
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157
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158 - 'Local database' for a 'Custom database search' (LocalCSVDatabaseSearchModule) step
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159
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160 Please open an issue if inputs for other steps are needed: https://github.com/galaxyproject/tools-iuc/issues/new
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161
0
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162 **Outputs**
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163
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164 Galaxy will store all outputs of MZMine in a single collection. When specifying the batch XML
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165 file one should pay attention to use file extensions that correspond to Galaxy datatypes
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166 (which allows Galaxy to easily autodetect the datatype). The following extensions can be used
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167 (lower/upper case does not matter):
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168
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169 - mzml
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170 - netcdf
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171 - mgf
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172 - txt
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173 - msp
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174 - csv
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175 - mztab
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176 - mztab2 (this is mzTab-m)
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177 - json
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178 - tabular (Galaxy's tsv implementation)
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179
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180 Specific datasets from the collection can be accessed using the *Extract dataset* tool, e.g.
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181 for further processing in Galaxy.
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182 ]]></help>
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183 <citations>
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184 <citation type="doi">10.1038/s41587-023-01690-2</citation>
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185 </citations>
1
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186 </tool>