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

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/main/tools/bioconductor-mzR commit 28f3d51cdd92c47c1a175029d73454708d487e73

<tool id="bioconductor_mzr_convert" name="bioconductor-mzR convert" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0" license="MIT">
    <description>mass spectrometry data conversion</description>
    <macros>
        <token name="@TOOL_VERSION@">2.40.0</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>

    <xrefs>
        <xref type="bio.tools">mzr</xref>
        <xref type="bioconductor">mzR</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bioconductor-mzr</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        Rscript '${bioconductor_mzr_convert}'
    ]]></command>

    <configfiles>
        <configfile name="bioconductor_mzr_convert"><![CDATA[
            #if $input_file.ext == $output_format:
            stop('Conversion from/to identical formats is not supported. Please select a different output format.')
            #end if

            #if $input_file.ext == "netcdf":
            backend <- "netCDF"
            #else
            backend <- "pwiz"
            #end if
            x <- mzR::openMSfile('$input_file', backend=backend)

            peaks <- mzR::peaks(x)
            header <- mzR::header(x)

            mzR::writeMSData(
                peaks,
                '$output_file',
                header=header,
                backend='pwiz',
                outformat = '$output_format',
                rtime_seconds = $rtime_seconds
            )
        ]]></configfile>
    </configfiles>
    <inputs>
        <param type="data" name="input_file" label="Input file" format="mzml,mzxml,netcdf" help="The input file to convert."/>
        <param type="select" name="output_format" label="Output format" display="radio" help="The format to convert the input file to.">
            <option value="mzml" selected="true">mzML</option>
            <option value="mzxml">mzXML</option>
        </param>
        <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."/>
    </inputs>
    <outputs>
        <data format="mzml" name="output_file">
            <change_format>
                <when input="output_format" value="mzxml" format="mzxml" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_file" location="https://zenodo.org/records/3757956/files/HU_neg_048.mzML" ftype="mzml"/>
            <param name="output_format" value="mzxml"/>
            <param name="rtime_seconds" value="FALSE"/>
            <output name="output_file">
                <assert_contents>
                    <has_n_lines n="38604"/>
                    <has_text text='msRun scanCount="2031" startTime="PT43.47S" endTime="PT68387.9S"'/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" location="https://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS200/FILES/OMAIR_012811_01.CDF" ftype="netcdf"/>
            <param name="output_format" value="mzml"/>
            <param name="rtime_seconds" value="TRUE"/>
            <output name="output_file">
                <assert_contents>
                    <has_n_lines n="162669"/>
                    <has_text text='run id="Experiment_1" defaultInstrumentConfigurationRef="IC"'/>
                    <has_text text='cvRef="MS" accession="MS:1000016" name="scan start time" value="0.154999997467" unitCvRef="UO" unitAccession="UO:0000010" unitName="second"'/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
===============================
bioconductor-mzR Convert Tool
===============================

**Description**

This tool converts mass spectrometry data files between supported formats (mzML, mzXML, netCDF) using the Bioconductor mzR package.
Conversion between identical formats is not supported.

Inputs
------

- **Input file**: Mass spectrometry data file in mzML, mzXML, or netCDF format.
- **Output format**: Choose the desired output format (mzML or mzXML).
- **Use retention time in seconds**: If enabled, retention times in the output will be reported in seconds (otherwise, in minutes).

Outputs
-------

- **Converted file**: The input file converted to the selected output format.
    ]]></help>
    <citations>
        <citation type="doi">10.18129/B9.bioc.mzR</citation>
        <citation type="doi">10.1038/nbt.2377</citation>
    </citations>
</tool>