comparison mzXMLShaper.xml @ 0:7c20fbf53fbf draft default tip

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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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>