annotate macros.xml @ 10:b80cc0382e70 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f10386dee95f3b1fbc8d1eeec52d450381ba89c5

<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.28.0</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="1.58.0" >bioconductor-camera</requirement>
           <requirement type="package" version="4.0.0" >bioconductor-xcms</requirement>
           <requirement type="package" version="1.30.0" >bioconductor-mspuritydata</requirement>
           <requirement type="package" version="1.7.5">r-optparse</requirement>
           <requirement type="package" version="1.4.7">r-rpostgres</requirement>
           <requirement type="package" version="0.10.27">r-rmysql</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="text-adduct-regex-validator">
	    <validator type="regex" message="Value may include alphanumeric characters, white space, commas, +, -, [ or ] ">[A-Za-z0-9,\[\] \+\-]+</validator>
    </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 99.5 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="FD-B">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="Note that when using 'scan' spectra types the spectraFilter option may need to be FALSE 
		      if 'allfrag' was not selecting when performing filterFragSpectra or if no filtering was performed at all" />
                <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="inter">Averaged inter spectra</option>
                        <option value="intra">Averaged intra spectra </option>
                        <option value="scan">All individual scans (may need to set spectraFilter to false with this option)</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>