comparison msnbase_readmsdata.xml @ 12:f6b2750ea32e draft

"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 3621a0c0a3a089fdb8973ae15a5614f32fa1d8df"

11:86a20118e743

<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.1">
    <description>Imports mass-spectrometry data files</description>

    <macros>
        <import>macros.xml</import>
        <import>macros_msnbase.xml</import>

    <command><![CDATA[
        @COMMAND_RSCRIPT@/msnbase_readmsdata.r

        #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
            singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
        #else
            zipfile '$input'
        #end if

        @COMMAND_LOG_EXIT@

generates an MSnExp object. This function uses the functionality
provided by the ‘mzR’ package to access data and meta data in
‘mzData’, ‘mzXML’ and ‘mzML’.

.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html
.. _here: http://web11.sb-roscoff.fr/download/w4m/howto/w4m_HowToPerformXcmsPreprocessing_v02.pdf


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Workflow position
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12:f6b2750ea32e

<tool id="msnbase_readmsdata" name="MSnbase readMSData" version="@WRAPPER_VERSION@.2">
    <description>Imports mass-spectrometry data files</description>

    <macros>
        <import>macros.xml</import>
        <import>macros_msnbase.xml</import>

    <command><![CDATA[
        @COMMAND_RSCRIPT@/msnbase_readmsdata.r

        #if $input.is_of_type("mzxml") or $input.is_of_type("mzml") or $input.is_of_type("mzdata") or $input.is_of_type("netcdf"):
            #if $os.path.islink(str($input))
                #set $source = $os.readlink(str($input))
                singlefile_galaxyPath '$source' singlefile_sampleName '$os.path.basename($source)'
            #else
                singlefile_galaxyPath '$input' singlefile_sampleName '$input.name'
            #end if
        #else
            zipfile '$input'
        #end if

        @COMMAND_LOG_EXIT@

generates an MSnExp object. This function uses the functionality
provided by the ‘mzR’ package to access data and meta data in
‘mzData’, ‘mzXML’ and ‘mzML’.

.. _xcms: https://bioconductor.org/packages/release/bioc/html/xcms.html


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Workflow position
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