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comparison 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
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children 90d60c9da21e
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-1:000000000000 0:02e802817d48
1 <tool id="mzmine_batch" name="MZMine batch" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <macros>
3 <token name="@TOOL_VERSION@">3.6.0</token>
4 <token name="@VERSION_SUFFIX@">0</token>
5 </macros>
6 <xrefs>
7 <xref type="bio.tools">mzmine</xref>
8 </xrefs>
9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">mzmine</requirement>
11 </requirements>
12 <command detect_errors="exit_code"><![CDATA[
13 #import re
14
15 mkdir -p input &&
16 #for $i in $input
17 #set escaped_i = re.sub('[^\s\w\-\.]', '_', str($i.element_identifier))
18 ln -s '$i' 'input/$escaped_i'.$i.ext &&
19 echo 'input/$escaped_i'.$i.ext >> input.txt &&
20 #end for
21
22 #if $libraries
23 mkdir -p libraries &&
24 #for $l in $libraries
25 #set escaped_l = re.sub('[^\s\w\-\.]', '_', str($l.element_identifier))
26 ln -s '$l' 'libraries/$escaped_l'.$l.ext &&
27 echo 'libraries/$escaped_l'.$l.ext >> libraries.txt &&
28 #end for
29 #end if
30 ## modify output paths in batch XML to relative path
31 ## - any output will be redirected to ./output/BASENAME
32 mkdir -p output/ &&
33
34 sed -e 's@<current_file>.*[\\\/]\([^\\\/]\+\)</current_file>@<current_file>./output/\1</current_file>@' '$batch' > batch.xml &&
35
36 mzmine
37 --batch 'batch.xml'
38 --input 'input.txt'
39 #if $libraries
40 --libraries 'libraries.txt'
41 #end if
42 --memory "\${MZMINE_MEMORY:-none}"
43 --temp "\${TMPDIR:-\$_GALAXY_JOB_TMP_DIR}"
44 --threads \${GALAXY_SLOTS:-1}
45 ## ignored parameters
46 ## -p,--pref <arg> preferences file
47 ## -r,--running keep MZmine running in headless mode
48 ## -tdfpseudoprofile Loads pseudo-profile frame spectra for tdf files
49 ## instead of centroided spectra.
50 ## -tsfprofile Loads profile spectra from .tsf data instead of
51 ## centroid spectra.
52 ]]></command>
53 <inputs>
54 <param argument="--batch" type="data" format="xml" label="MZMine batch file" help="XML batch file (ideally created with version @TOOL_VERSION@)"/>
55 <param argument="--input" type="data" format="mzml,mzxml,csv" multiple="true" label="Spectra (mzml)"/>
56 <param argument="--libraries" type="data" format="json,mgf,msp" multiple="true" optional="true" label="Spectral libraries"/>
57 </inputs>
58 <outputs>
59 <collection name="output" type="list">
60 <discover_datasets pattern="__name_and_ext__" directory="output"/>
61 </collection>
62 </outputs>
63 <tests>
64 <test>
65 <param name="batch" value="test_small.xml" ftype="xml"/>
66 <param name="input" value="DOM_a.mzML,DOM_b.mzXML"/>
67 <param name="libraries" value="GNPS-FAULKNERLEGACY.json" ftype="json"/>
68 <!-- <param name="input" location="https://raw.githubusercontent.com/mzmine/mzmine3/master/src/test/resources/rawdatafiles/DOM_a.mzML"/> -->
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"/>
70 <param name="libraries" location="https://external.gnps2.org/gnpslibrary/GNPS-FAULKNERLEGACY.json" ftype="json"/> -->
71 <output_collection name="output" count="3" type="list">
72 <element name="test2_iimn_gnps" ftype="mgf">
73 <assert_contents>
74 <has_n_lines n="2103"/>
75 <has_text text="BEGIN IONS"/>
76 </assert_contents>
77 </element>
78 <element name="test2_iimn_gnps_quant" ftype="csv">
79 <assert_contents>
80 <has_n_lines n="34"/>
81 <has_n_columns sep="," n="16"/>
82 </assert_contents>
83 </element>
84 <element name="test2_sirius" ftype="mgf">
85 <assert_contents>
86 <has_n_lines n="54406"/>
87 <has_text text="BEGIN IONS"/>
88 </assert_contents>
89 </element>
90 </output_collection>
91 </test>
92 </tests>
93 <help><![CDATA[
94 MZmine 3 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data.
95
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
97 and use this to execute such an analysis on the Galaxy platform.
98
99 **Inputs**
100
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@).
102 - Input spectra in mzml format
103 - Spectra libraries in mgf or json format (optional)
104
105 **Outputs**
106
107 Galaxy will store all outputs of MZMine in a single collection. When specifying the batch XML
108 file one should pay attention to use file extensions that correspond to Galaxy datatypes
109 (which allows Galaxy to easily autodetect the datatype). The following extensions can be used
110 (lower/upper case does not matter):
111
112 - mzml
113 - netcdf
114 - mgf
115 - txt
116 - msp
117 - csv
118 - mztab
119 - mztab2 (this is mzTab-m)
120 - json
121 - tabular (Galaxy's tsv implementation)
122
123 Specific datasets from the collection can be accessed using the *Extract dataset* tool, e.g.
124 for further processing in Galaxy.
125 ]]></help>
126 <citations>
127 <citation type="doi">10.1038/s41587-023-01690-2</citation>
128 </citations>
129 </tool>