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comparison bioconductor_mzr_convert.xml @ 0:42e59b8e9e0b draft default tip

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/main/tools/bioconductor-mzR commit 28f3d51cdd92c47c1a175029d73454708d487e73
author recetox
date Thu, 19 Jun 2025 08:17:53 +0000
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-1:000000000000 0:42e59b8e9e0b
1 <tool id="bioconductor_mzr_convert" name="bioconductor-mzR convert" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
2 <description>mass spectrometry data conversion</description>
3 <macros>
4 <token name="@TOOL_VERSION@">2.40.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7
8 <xrefs>
9 <xref type="bio.tools">mzr</xref>
10 <xref type="bioconductor">mzR</xref>
11 </xrefs>
12 <requirements>
13 <requirement type="package" version="@TOOL_VERSION@">bioconductor-mzr</requirement>
14 </requirements>
15 <command detect_errors="exit_code"><![CDATA[
16 Rscript '${bioconductor_mzr_convert}'
17 ]]></command>
18
19 <configfiles>
20 <configfile name="bioconductor_mzr_convert"><![CDATA[
21 #if $input_file.ext == $output_format:
22 stop('Conversion from/to identical formats is not supported. Please select a different output format.')
23 #end if
24
25 #if $input_file.ext == "netcdf":
26 backend <- "netCDF"
27 #else
28 backend <- "pwiz"
29 #end if
30 x <- mzR::openMSfile('$input_file', backend=backend)
31
32 peaks <- mzR::peaks(x)
33 header <- mzR::header(x)
34
35 mzR::writeMSData(
36 peaks,
37 '$output_file',
38 header=header,
39 backend='pwiz',
40 outformat = '$output_format',
41 rtime_seconds = $rtime_seconds
42 )
43 ]]></configfile>
44 </configfiles>
45 <inputs>
46 <param type="data" name="input_file" label="Input file" format="mzml,mzxml,netcdf" help="The input file to convert."/>
47 <param type="select" name="output_format" label="Output format" display="radio" help="The format to convert the input file to.">
48 <option value="mzml" selected="true">mzML</option>
49 <option value="mzxml">mzXML</option>
50 </param>
51 <param type="boolean" name="rtime_seconds" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Use retention time in seconds" help="If checked, the retention time will be reported in seconds. If unchecked, it will be reported in minutes. Note that no active conversion is taking place."/>
52 </inputs>
53 <outputs>
54 <data format="mzml" name="output_file">
55 <change_format>
56 <when input="output_format" value="mzxml" format="mzxml" />
57 </change_format>
58 </data>
59 </outputs>
60 <tests>
61 <test>
62 <param name="input_file" location="https://zenodo.org/records/3757956/files/HU_neg_048.mzML" ftype="mzml"/>
63 <param name="output_format" value="mzxml"/>
64 <param name="rtime_seconds" value="FALSE"/>
65 <output name="output_file">
66 <assert_contents>
67 <has_n_lines n="38604"/>
68 <has_text text='msRun scanCount="2031" startTime="PT43.47S" endTime="PT68387.9S"'/>
69 </assert_contents>
70 </output>
71 </test>
72 <test>
73 <param name="input_file" location="https://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS200/FILES/OMAIR_012811_01.CDF" ftype="netcdf"/>
74 <param name="output_format" value="mzml"/>
75 <param name="rtime_seconds" value="TRUE"/>
76 <output name="output_file">
77 <assert_contents>
78 <has_n_lines n="162669"/>
79 <has_text text='run id="Experiment_1" defaultInstrumentConfigurationRef="IC"'/>
80 <has_text text='cvRef="MS" accession="MS:1000016" name="scan start time" value="0.154999997467" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"'/>
81 </assert_contents>
82 </output>
83 </test>
84 </tests>
85 <help><![CDATA[
86 ===============================
87 bioconductor-mzR Convert Tool
88 ===============================
89
90 **Description**
91
92 This tool converts mass spectrometry data files between supported formats (mzML, mzXML, netCDF) using the Bioconductor mzR package.
93 Conversion between identical formats is not supported.
94
95 Inputs
96 ------
97
98 - **Input file**: Mass spectrometry data file in mzML, mzXML, or netCDF format.
99 - **Output format**: Choose the desired output format (mzML or mzXML).
100 - **Use retention time in seconds**: If enabled, retention times in the output will be reported in seconds (otherwise, in minutes).
101
102 Outputs
103 -------
104
105 - **Converted file**: The input file converted to the selected output format.
106 ]]></help>
107 <citations>
108 <citation type="doi">10.18129/B9.bioc.mzR</citation>
109 <citation type="doi">10.1038/nbt.2377</citation>
110 </citations>
111 </tool>