Mercurial > repos > workflow4metabolomics > mzxmlshaper
comparison mzXMLShaper.xml @ 0:7c20fbf53fbf draft default tip
planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics commit f85839922690f81d3ec5876d1b7981e76e36d363
author | workflow4metabolomics |
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date | Mon, 07 Oct 2024 11:40:19 +0000 |
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1 <tool id="mzxmlshaper" name="Mz(X)ML Shaper" version="1.0.0+galaxy0" profile="21.01"> | |
2 <description> | |
3 conversion into XCMS-supported mz(X)ML file formats | |
4 </description> | |
5 <requirements> | |
6 <requirement type="package" version="4.3.3">r-base</requirement> | |
7 <requirement type="package" version="0.42.0">bioconductor-msdata</requirement> | |
8 <requirement type="package" version="2.36.0">bioconductor-mzr</requirement> | |
9 <requirement type="package" version="1.0.0">r-w4mrutils</requirement> | |
10 </requirements> | |
11 <command detect_errors="aggressive"><![CDATA[ | |
12 Rscript '$__tool_directory__/mzXMLShaper.R' | |
13 inputfilename '$infile' | |
14 outputfileformat '$outformat' | |
15 #if str($outformat) == 'mzml': | |
16 outputfilename '$mzml_file' | |
17 #elif str($outformat) == 'mzXml': | |
18 outputfilename '$mzXml_file' | |
19 #end if | |
20 ]]></command> | |
21 <inputs> | |
22 <param name="infile" type="data" format="mzml,mzxml,netcdf" label="File(s) to convert" help="file or collection"/> | |
23 <param name="outformat" type="select" label="Desired output format"> | |
24 <option value="mzml">mzML</option> | |
25 <option value="mzXml">mzXML</option> | |
26 </param> | |
27 </inputs> | |
28 <outputs> | |
29 <data format="mzml" label="${infile.name}_converted.mzml" name="mzml_file"> | |
30 <filter>outformat=="mzml"</filter> | |
31 </data> | |
32 <data format="mzxml" label="${infile.name}_converted.mzxml" name="mzXml_file"> | |
33 <filter>outformat=="mzXml"</filter> | |
34 </data> | |
35 </outputs> | |
36 <tests> | |
37 <test expect_num_outputs="1"> | |
38 <param name="infile" value="original_data/ko16.CDF"/> | |
39 <param name="outformat" value="mzml"/> | |
40 <output name="mzml_file" file="conversion_result_cdf_to_mzml.mzml" /> | |
41 </test> | |
42 <test expect_num_outputs="1"> | |
43 <param name="infile" value="original_data/ko16.CDF"/> | |
44 <param name="outformat" value="mzXml"/> | |
45 <output name="mzXml_file" file="conversion_result_cdf_to_mzxml.mzxml"/> | |
46 </test> | |
47 <test expect_num_outputs="1"> | |
48 <param name="infile" value="original_data/ko16.mzXml"/> | |
49 <param name="outformat" value="mzml"/> | |
50 <output name="mzml_file" file="conversion_result_mzxml_to_mzml.mzml" /> | |
51 </test> | |
52 <test expect_num_outputs="1"> | |
53 <param name="infile" value="original_data/ko16.mzXml"/> | |
54 <param name="outformat" value="mzXml"/> | |
55 <output name="mzXml_file" file="conversion_result_mzxml_to_mzxml.mzxml"/> | |
56 </test> | |
57 <test expect_num_outputs="1"> | |
58 <param name="infile" value="original_data/ko16.mzml"/> | |
59 <param name="outformat" value="mzml"/> | |
60 <output name="mzml_file" file="conversion_result_mzml_to_mzml.mzml" /> | |
61 </test> | |
62 <test expect_num_outputs="1"> | |
63 <param name="infile" value="original_data/ko16.mzml"/> | |
64 <param name="outformat" value="mzXml"/> | |
65 <output name="mzXml_file" file="conversion_result_mzml_to_mzxml.mzxml"/> | |
66 </test> | |
67 </tests> | |
68 <help><![CDATA[ | |
69 .. class:: infomark | |
70 | |
71 **Credits** | |
72 | **Original tool wrapping:** Quentin Ruin - INRAE - MetaboHUB | |
73 | **Tool maintainer:** Mélanie Pétéra - INRAE - MetaboHUB | |
74 | |
75 .. class:: infomark | |
76 | |
77 **Help and support:** https://community.france-bioinformatique.fr/c/workflow4metabolomics/10 | |
78 | |
79 --------------------------------------------------- | |
80 | |
81 ****************** | |
82 Mz(X)ML Shaper | |
83 ****************** | |
84 =========== | |
85 DESCRIPTION | |
86 =========== | |
87 | |
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). | |
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. | |
90 For more information about this package, see the related documentation (https://bioconductor.org/packages/release/bioc/html/mzR.html) | |
91 | |
92 --------------------------------------------------- | |
93 | |
94 ========================== | |
95 ALIGNMENT WITH OTHER TOOLS | |
96 ========================== | |
97 | |
98 ----------- | |
99 INPUT FILES | |
100 ----------- | |
101 | |
102 Open format MS files (.netCDF, .mzML, .mzXML) | |
103 | |
104 ------------ | |
105 OUTPUT FILES | |
106 ------------ | |
107 | |
108 A file (or collection of files) converted in mzML or mzXML with the same name as the input file (except for the extension) | |
109 | |
110 ---------------------------- | |
111 EXAMPLE OF WORKFLOW POSITION | |
112 ---------------------------- | |
113 | |
114 Used as first step in any workflow supporting mzML or mzXML formats just before ReadMSData. | |
115 | |
116 --------------------------------------------------- | |
117 | |
118 =============== | |
119 TOOL PARAMETERS | |
120 =============== | |
121 | |
122 - Desired output format: mzML or MZXML | |
123 | |
124 --------------------------------------------------- | |
125 | |
126 ================== | |
127 OUTPUT DESCRIPTION | |
128 ================== | |
129 | |
130 Standardized MzML or mzXML files (depending on the user's configuration of the tool) | |
131 | |
132 --------------------------------------------------- | |
133 | |
134 ============== | |
135 EXAMPLE OF USE | |
136 ============== | |
137 | |
138 .netCDF file upload -> Mz(X)MLShaper -> ReadMSData -> any workflow | |
139 | |
140 ------------ | |
141 KNOWN ISSUES | |
142 ------------ | |
143 | |
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. | |
145 | |
146 ]]> | |
147 </help> | |
148 <citations> | |
149 <citation type="doi">10.18129/B9.bioc.mzR</citation> | |
150 </citations> | |
151 </tool> |