annotate macros.xml @ 2:a11892cb997d draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 242de155f13acd6cb88946e89b5196ac55578aa8"

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.12.2</token>
    <token name="@GALAXY_TOOL_VERSION@">0</token>

    <xml name="requirements">
        <requirements>
           <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement>
           <requirement type="package" version="1.42.0" >bioconductor-camera</requirement>
           <requirement type="package" version="3.8.0" >bioconductor-xcms</requirement>
           <requirement type="package" version="1.14.0" >bioconductor-mspuritydata</requirement>
           <requirement type="package" version="1.6.4">r-optparse</requirement>
           <requirement type="package" version="1.1.1">r-rpostgres</requirement>
           <requirement type="package" version="0.10.17">r-rmysql</requirement>
            <yield />
        </requirements>
    </xml>


    <xml name="offsets">
        <param argument="--minoffset" type="float" label="minoffset" value="0.5"
               help="Offset to the 'left' for the precursor range e.g. if precursor of interest is
               100.0 then the range would be from 999.5 to 100.0"/>
        <param argument="--maxoffset" type="float" label="maxoffset" value="0.5"
               help="Offset to the 'right' for the precursor range  e.g. if precursor of interest is
               100.0 then the range would be from 100.0 to 100.5"/>
    </xml>
    <xml name="general_params">
        <param argument="--ilim" type="float" value="0.05" 
               label="Threshold to remove peaks below x % of the relative intensity of
               precursor of interest"
               help="All peaks less than this percentage of the precursor ion of interest will be
               removed from the purity calculation, default is 5\% (0.05).
               Essentially a noise filter to remove peaks that are thought to have either none or
               very limited impact on the resulting fragmentation spectra."/>
        <param argument="--iw_norm" type="select" label="Normalisation for isolation efficiency">
                <option value="gauss" >Gaussian</option>
                <option value="rcosine" >Raised cosine</option>
                <option value="QE5"> Calculated from Q-Exactive for +/- 0.5 Da windows </option>
                <option value="none" selected="true" >No normalisation</option>
        </param>
        <conditional name="isotopes">
            <param argument="--isotopes" type="select" label="Handling of isotopic peaks" >
                <option value="keep" >Keep isotopes in precursor ion purity calculation</option>
                <option value="exclude_default" selected="true" >Exclude C12/C13 isotopes in precursor ion purity calculation</option>
                <option value="user" >Exclude a user supplied list of isotopes in purity calculation</option>
            </param>
            <when value="keep">
            </when>
            <when value="exclude_default">
            </when>
            <when value="user">
                <param argument="--im" type="data" format="tabular" label="Isotope matrix" help="
                 tabular file composing of columns:
                  ['isotope_id', 'mass diff', 'abundance of isotope', 'ppm tol for mz', 'abundance buffer',
                                  'charge', 'relative atomic mass (int)', 'xflag'].
                The xflag indicates if the larger (mass) isotope is the most abundant or less abundant.
                e.g. for c12 to c13, the c13 is less abundant so we flag as 1 for Li6 to Li7, the Li7 is more abundant
                so we would flag as 0.
                Example row: For C13 isotope (single charge) the row could be [1, 1.003355, 1.07, 4, 0.1, 1, 12, 1]"/>
            </when>
        </conditional>
    </xml>


    <xml name="camera_xcms">
            <param argument="--camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?"
               help="Within the RData file there should be either an XCMS object called xset or a CAMERA object called
                      xa (or both). The XCMS object is nested within the CAMERA object so either can be used">
                <option value="xcms" selected="true" >XCMS (xset)</option>
                <option value="camera" >CAMERA (xa)</option>
        </param>
    </xml>


    <xml name="fileload">
            <conditional name="file_load_conditional">
                <param name="file_load_select" type="select" label="Resubmit your dataset"
                       help="Use only if you get a message which say that your original dataset or
                                dataset collection can not be found the server." >
                    <option value="no" >no need</option>
                    <option value="yes" >yes</option>
                </param>
                <when value="no">
                </when>
                <when value="yes">
                    <param name="input" type="data_collection" collection_type="list"  format="mzxml,mzml,mzdata,netcdf"
                           multiple="true" label="File(s) from your history containing your chromatograms"
                           help="Select the dataset collection containing the files that were used
                                 for processing" />
                </when>
        </conditional>
    </xml>

    <xml name="grp_peaklist">
        <conditional name="grp_peaklist_opt">
            <param name="grp_peaklist_opt" type="select" label="Add a different grouped peaklist to database?">
                <option value="yes" >Provide group peaklist </option>
                <option value="no" selected="true">Use default grouped peaklist</option>
            </param>
            <when value="no">
            </when>
            <when value="yes">
                <param argument="--grp_peaklist" type="data" label="grouped peaklist"
                    help="User supplied grouped peaklist to add to the database (if additional columns required e.g.
                          CAMERA annotations" format="tsv,tabular"/>
            </when>
        </conditional>
    </xml>

    <xml name="sm_input" token_ql='Query' token_dblabel="SQLite database"  token_ql_shrt="Q"
         token_user="True" token_mspuritydatalib="False" token_msp="False" token_help="">
        <conditional name="@QL_SHRT@_dbPth_con">
            <param argument="--@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" >
                <option value="sqlite" selected="@USER@" >SQLite database of (LC)-MS/MS data</option>
                <option value="local_config" selected="@USER@" >Locally configured SQLite, MySQL or PostgreSQL database</option>
                <option value="msPurityData"  selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option>
            </param>
            <when value="sqlite">
               <param argument="--@QL_SHRT@_dbPth" type="data" label="@QL@ SQLite database" format="sqlite" help=""/>
            </when>
            <when value="local_config">
            </when>
            <when value="msPurityData">
            </when>
        </conditional>
    </xml>


    <xml name="filters" token_ql="Query" token_polarity_positive="false" token_ql_shrt="Q"
         token_sources_select="false" token_instrument_types_select="false">

        <section name="@QL_SHRT@_filters" title="Filters" expanded="False">

            <param argument="--@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/>
            <param argument="--@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/>

            <conditional name="@QL_SHRT@_raThres_cond">
                <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/>
                <when value="true">
                    <param argument="--@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/>
                </when>
                <when value="false">
                </when>
            </conditional>

            <conditional name="@QL_SHRT@_polarity_cond">
                <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" />
                <when value="true">
                    <param argument="--@QL_SHRT@_polarity" type="select" label="Polarity" multiple="true" >
                      <option value="positive" selected="@POLARITY_POSITIVE@">Positive</option>
                      <option value="negative" >Negative</option>
                      <option value="NA" >NA</option>
                    </param>
                </when>
                <when value="false">
                </when>
            </conditional>

            <conditional name="@QL_SHRT@_purity_cond">
                <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/>
                <when value="true">
                    <param argument="--@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6"
                           label="Precursor ion purity threshold"/>
                </when>
                <when value="false">
                </when>
            </conditional>

            <conditional name="@QL_SHRT@_xcmsGroups_cond">
                <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/>
                <when value="true">
                    <param argument="--@QL_SHRT@_xcmsGroups" type="text" value=""
                          label="XCMS group ids of spectra"
                          help="comma seperated list of grpids (correspond to column 'grpid in c_peak_group'))
                                e.g '12,27,30'" />
                </when>
                <when value="false">
                </when>
            </conditional>


            <conditional name="@QL_SHRT@_pids_cond">
                <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/>
                <when value="true">
                    <param argument="--@QL_SHRT@_pids" type="text" value=""
                          label="pids of spectra (correspond to column 'pid; in s_peak_meta)"
                          help="comma seperated list of pids (correspond to column 'pid; in s_peak_meta))
                                e.g '3001,5561'" />
                </when>
                <when value="false">
                </when>
            </conditional>


            <conditional name="@QL_SHRT@_rtrange_cond">
                <param name="@QL_SHRT@_rtrange_bool" type="boolean"
                       label="Filter on retention time range?"
                       help="Filter the spectra between two points of retention time range"/>
                <when value="true">
                    <param argument="--@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)"
                           type="float" value="0" help=""/>
                    <param argument="--@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)"
                           type="float" value="3000" help=""/>
                </when>
                <when value="false">
                </when>
            </conditional>



            <conditional name="@QL_SHRT@_accessions_cond">
                <param name="@QL_SHRT@_accessions_bool" type="boolean"
                       label="Filter on accessions?"
                       help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/>
                <when value="true">
                    <param argument="--@QL_SHRT@_accessions" type="text" value=""
                          label="Spectra accessions"
                          help="Comma seperated list of accessions))
                                e.g 'AC000001,BS001003,LIT00001'" />
                </when>
                <when value="false">
                </when>
            </conditional>


            <conditional name="@QL_SHRT@_sources_cond">
                <param name="@QL_SHRT@_sources_bool" type="boolean"
                       label="Filter on sources?" help="" value="@SOURCES_SELECT@" />
                <when value="true">
                    <param argument="--@QL_SHRT@_sources" type="select" multiple="true"
                       help="@QL_SHRT@ The default internal SQLite database of library (reference) spectra
                       contains fragmentation spectra from MassBank, LipidBlast and GNPS. A copy is
                       available from here:
                       https://bioconductor.org/packages/release/data/experiment/html/msPurityData.html" >
                        <option value="massbank" selected="true">MassBank from MoNa</option>
                        <option value="gnps" selected="true">GNPS</option>
                        <option value="hmdb" selected="true">HMDB</option>
                        <option value="lipidblast" selected="true">LipidBlast</option>
                    </param>
                    <param name="@QL_SHRT@_sourcesUser" type="text" label="Sources - user specific" value=""
                      help="comma seperated list of additional sources (e.g. if the user has other
                      sources - like there own personal library)
                      e.g 'LIPIDS_03052019,HILIC_03052019'" />
                </when>
                <when value="false">
                </when>
            </conditional>
            <conditional name="@QL_SHRT@_instrumentTypes_cond">
                <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean"
                       value="@INSTRUMENT_TYPES_SELECT@"
                       label="Filter on instrument type?" help="" />
                <when value="true">
                    <param argument="--@QL_SHRT@_instrumentTypes" type="select" multiple="true"
                       help="" >
                        <option value="APCI-ITFT" selected="true" >APCI-ITFT</option>
                        <option value="APCI-ITTOF" selected="true" >APCI-ITTOF</option>
                        <option value="CE-ESI-TOF" selected="true" >CE-ESI-TOF</option>
                        <option value="CI-B">CI-B</option>
                        <option value="EI-B">EI-B</option>
                        <option value="EI-EBEB">EI-EBEB</option>
                        <option value="ESI-ITFT" selected="true" >ESI-ITFT</option>
                        <option value="ESI-ITTOF" selected="true" >ESI-ITTOF</option>
                        <option value="ESI-QFT" selected="true" >ESI-QFT</option>
                        <option value="ESI-QTOF" selected="true" >ESI-QTOF</option>
                        <option value="ESI-TOF" selected="true" >ESI-TOF</option>
                        <option value="FAB-B">FAB-B</option>
                        <option value="FAB-BE">FAB-BE</option>
                        <option value="FAB-EB">FAB-EB</option>
                        <option value="FAB-EBEB">FAB-EBEB</option>
                        <option value="FAB-EBEB">FD-B</option>
                        <option value="FI-B">FI-B</option>
                        <option value="Flow-injection QqQ/MS">Flow-injection QqQ/MS</option>
                        <option value="GC-EI-Q">GC-EI-Q</option>
                        <option value="GC-EI-QQ">GC-EI-QQ</option>
                        <option value="GC-EI-TOF">GC-EI-TOF</option>
                        <option value="GC-MS">GC-MS</option>
                        <option value="Hybrid FT">Hybrid FT</option>
                        <option value="in source CID" selected="true" >in source CID</option>
                        <option value="In-silico QTOF" selected="true" >In-silico QTOF</option>
                        <option value="Ion trap" selected="true" >Ion trap</option>
                        <option value="LC-APCI-ITFT" selected="true" >LC-APCI-ITFT</option>
                        <option value="LC-APCI-QTOF" selected="true" >LC-APCI-QTOF</option>
                        <option value="LC-APCI-Q" selected="true">LC-APCI-Q</option>
                        <option value="LC-APPI-QQ">LC-APPI-QQ</option>
                        <option value="LC-ESI-IT" selected="true">LC-ESI-IT</option>
                        <option value="LC-ESI-ITFT" selected="true">LC-ESI-ITFT</option>
                        <option value="LC-ESI-ITTOF" selected="true">LC-ESI-ITTOF</option>
                        <option value="LC-ESI-Q" selected="true">LC-ESI-Q</option>
                        <option value="LC-ESI-QFT" selected="true">LC-ESI-QFT</option>
                        <option value="LC-ESI-QIT" selected="true">LC-ESI-QIT</option>
                        <option value="LC-ESI-QQ" selected="true">LC-ESI-QQ</option>
                        <option value="LC-ESI-QTOF" selected="true">LC-ESI-QTOF</option>
                        <option value="LC-ESI-TOF" selected="true">LC-ESI-TOF</option>
                        <option value="LC-Q-TOF/MS" selected="true">LC-Q-TOF/MS</option>
                        <option value="LC-QTOF" selected="true">LC-QTOF</option>
                        <option value="Linear Ion Trap" selected="true">Linear Ion Trap</option>
                        <option value="LIT" selected="true">LIT</option>
                        <option value="MALDI-QIT" selected="true">MALDI-QIT</option>
                        <option value="MALDI-TOF" selected="true">MALDI-TOF</option>
                        <option value="MALDI-TOFTOF" selected="true">MALDI-TOFTOF</option>
                        <option value="orbitrap" selected="true">orbitrap</option>
                        <option value="QIT" selected="true">QIT</option>
                        <option value="QIT-FT" selected="true">QIT-FT</option>
                        <option value="QIT-TOF" selected="true">QIT-TOF</option>
                        <option value="QqQ" selected="true">QqQ</option>
                        <option value="Q-TOF" selected="true">Q-TOF</option>
                        <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option>
                        <option value="none">None</option>
                  </param>
                  <param argument="--@QL_SHRT@_instrumentTypesUser" type="text" value=""
                         help="Types of the instruments to be included in the search. Use a comma to
                               separate the instrument types or leave empty to ignore filter."/>
                </when>
                <when value="false">
                </when>
            </conditional>
            <conditional name="@QL_SHRT@_instruments_cond">
                <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" />
                <when value="true">
                    <param argument="--@QL_SHRT@_instruments" type="text" value=""
                         help="Known instrument names to filter on. Use a comma to
                               separate the instrument types or leave empty to ignore filter."/>
                </when>
                <when value="false">
                </when>
            </conditional>



            <conditional name="@QL_SHRT@_spectraTypes_cond">
                <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?"
                help="" />
                <when value="true">
                    <param argument="--@QL_SHRT@_spectraTypes" type="select" multiple="true"  label="Spectra type" >
                        <option value="av_all" selected="true">Averaged all spectra ignoring inter-intra relationships </option>
                        <option value="av_inter">Averaged inter spectra</option>
                        <option value="av_intra">Averaged intra spectra </option>
                        <option value="scans">All individual scans</option>
                        <option value="NA">Not applicable/defined</option>
                    </param>
                </when>
                <when value="false">
                </when>
            </conditional>

           <param argument="--@QL_SHRT@_spectraFilter" type="boolean" checked="true"
                  label="Ignore any peaks flagged in the spectra in previous stages?"
                          help="" />

        </section>
    </xml>




    <xml name="citations">
        <citations>
            <citation type="doi">10.1021/acs.analchem.6b04358</citation>
            <yield />
        </citations>
    </xml>

</macros>