Mercurial > repos > computational-metabolomics > mspurity_createmsp
diff macros.xml @ 0:35898942bfbb draft
"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc-dirty"
| author | computational-metabolomics |
|---|---|
| date | Wed, 27 Nov 2019 14:20:07 -0500 |
| parents | |
| children | d1d73007a255 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 27 14:20:07 2019 -0500 @@ -0,0 +1,364 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">1.12.0</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="1.42.0" >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>