view createMSP.xml @ 11:4b3b0f5a55d9 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3

<tool id="mspurity_createmsp" name="msPurity.createMSP" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
    <description>Create MSP files from msPurity processed data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
    </expand>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript" ><![CDATA[
    createMSP.R
    --rdata_input "$rdata_input"
    --method "$method"

    #if $metadata_cond.metadata_select == "true"
        --metadata "$metadata_cond.metadata"
        --metadata_cols "$metadata_cond.metadata_cols"
        --adduct_split "$metadata_cond.adduct_split"
    #end if

    #if $xcms_group_cond.xcms_group_select == "true"
        --xcms_groupids "$xcms_group_cond.xcms_groupids"
    #end if

    $filter

    --msp_schema "$msp_schema"
    --intensity_ra "$intensity_ra"

    --out_dir '.'
    ]]></command>
    <inputs>
        <param name="rdata_input" type="data" format="rdata" label="msPurity purityA dataset" argument="--purity_dataset"
        help="RData file containing the purityA object following frag4feature and/or averageFragmentation"/>
        <param name="method" type="select" label="How to choose fragmentation spectra (if precursor was fragmented in >1 scans per XCMS group feature)"
        help="'Average all' will use the averaged MS/MS spectra of the XCMS grouped feature, ignoring inter and intra file relationships,
             'Average' (intra)' will use the intra file (within file) averaged MS/MS spectra of the XCMS grouped feature,
             'Average (inter)' will use the inter file (across file) MS/MS averaged spectra,
             'All scans' will export all matching MS/MS spectra to XCMS grouped features,
             'Max intensity' will choose the most MS/MS spectra with the most intense precursor ion for each XCMS grouped feature"
             argument="--method">
            <option value="av_all" selected="true">Average (all)</option>
            <option value="av_intra">Average (intra)</option>
            <option value="av_inter">Average (inter)</option>
            <option value="all">All scans</option>
            <option value="max" >Max intensity</option>
        </param>

        <conditional name="metadata_cond">
            <param name="metadata_select" type="boolean" label="Use additional metadata?" />
	    <when value="true">
                <param type="data" name="metadata" label="Metadata for each feature" format="tsv,tabular"
                help="Metadata for each grouped XCMS feature, the data will be added to the MSP metadata.
                Using the MassBank format e.g. https://github.com/MassBank/MassBank-data/blob/master/MetaboLights/ML003001.txt "/>

                <param name="metadata_cols" type="text" label="Metadata columns for name" value="CH$NAME, MS$FOCUSED_ION: PRECURSOR_TYPE" help="Comma separated string of column names where the corresponding values in the metadata will be used for the MSP spectra name"/>
                <param name="adduct_split" type="boolean" checked="true" label="Create MSP spectra for each adduct?" help="If either 'adduct' or 'MS$FOCUSED_ION: PRECURSOR_TYPE'
                    column is in metadata then each adduct will have it's own MSP spectra.
                    (Useful, if the MSP file will be used for further annotation)"  />
            </when>
            <when value="false">
            </when>
        </conditional>

        <conditional name="xcms_group_cond">
            <param name="xcms_group_select" type="boolean" label="Select XCMS groups?" help="if set to no, all XCMS group features will be used" />
            <when value="true">
                <param name="xcms_groupids" type="text" label="XCMS peak group ids" value=""
                help="Comma separated string of XCMS group ids to export MSP spectra for. If blank all XCMS peak groups will be used"/>
            </when>
            <when value="false">
            </when>
        </conditional>

        <param name="intensity_ra" type="select" label="Include intensity, relative abundanace or both in the MSP file"
             argument="--intensity_ra">
            <option value="intensity_ra" selected="true">Both intensity and relative abundance</option>
            <option value="intensity">Intensity only</option>
            <option value="ra">Relative abundance only</option>
        </param>

        <param name="msp_schema" type="select" label="MSP schema to use for files"
             argument="--msp_schema">
            <option value="massbank" selected="true">MassBank (Europe)</option>
            <option value="mona">MoNA</option>

        </param>

        <param name="filter" type="boolean" checked="true" truevalue="--filter" falsevalue="" label="Filter peaks that have been flagged in prior processing steps"   help="" />

    </inputs>
    <outputs>
        <data name="createMSP_output" format="msp" from_work_dir="lcmsms_spectra.msp" label="${tool.name} on ${on_string}: msp"/>
    </outputs>
    <tests>
        <test>
            <param name="method" value="all"/>
            <param name="rdata_input" value="frag4feature_output.RData"/>
            <output name="createMSP_output" file="createMSP_output_scans_all.msp"/>
        </test>
        <test>
            <param name="method" value="av_all"/>
            <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
            <output name="createMSP_output" file="createMSP_output_av_all.msp"/>
        </test>
        <test>
            <param name="method" value="av_all"/>
            <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
            <param name="metadata_cond|metadata_select" value="true"/>
            <param name="metadata_cond|metadata" value="createMSP_input_metadata.tsv"/>
            <param name="metadata_cond|metadata_cols" value="AC$CHROMATOGRAPHY: COLUMN_NAME, AC$MASS_SPECTROMETRY: ION_MODE, AC$MASS_SPECTROMETRY: MS_TYPE, CH$LINK: INCHIKEY, CH$LINK: PUBCHEM	CH$NAME
"/>
            <param name="xcms_group_cond|xcms_group_select" value="true"/>
            <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
            <param name="metadata_cond|adduct_split" value="true"/>
            <output name="createMSP_output" file="createMSP_output_av_all_metadata.msp"/>
        </test>
        <test>
            <param name="method" value="av_all"/>
            <param name="rdata_input" value="averageFragSpectra_output_all.RData"/>
            <param name="xcms_group_cond|xcms_group_select" value="true"/>
            <param name="xcms_group_cond|xcms_groupids" value="8,12"/>
            <output name="createMSP_output" file="createMSP_output_av_all_and_all_xcms.msp"/>
        </test>
        <test>
            <param name="method" value="av_intra"/>
            <param name="rdata_input" value="averageFragSpectra_output_intra.RData"/>
            <output name="createMSP_output" file="createMSP_output_av_intra.msp"/>
        </test>
        <test>
            <param name="method" value="av_inter"/>
            <param name="rdata_input" value="averageFragSpectra_output_inter.RData"/>
            <output name="createMSP_output" file="createMSP_output_av_inter.msp"/>
        </test>
        <test>
            <param name="method" value="max"/>
            <param name="rdata_input" value="frag4feature_output.RData"/>
            <output name="createMSP_output" file="createMSP_output_max.msp"/>
        </test>
    </tests>
	<help><![CDATA[
------------------------------
Create MSP Files from msPurity
------------------------------

Description
-----------

| This tool will extract the MSMS spectra data from an msPurity-frag4feature object into a file with MSP data format.




Developers and contributors
---------------------------

- **Jordi Capellades ([e-mail]) - Universitat Rovira i Virgili (SP)**
- **Andris Jankevics ([e-mail]) - University of Birmingham (UK)**
- **Thomas N. Lawson ([e-mail]) - University of Birmingham (UK)**
- **Ralf Weber ([e-mail]) - University of Birmingham (UK)**

	]]></help>

<expand macro="citations" />

</tool>