Mercurial > repos > tomnl > mspurity_frag4feature
diff macros.xml @ 15:a2ba12977060 draft default tip
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
| author | tomnl |
|---|---|
| date | Wed, 27 Nov 2019 12:35:23 +0000 |
| parents | 64431b9affe2 |
| children |
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--- a/macros.xml Fri Sep 27 09:21:47 2019 -0400 +++ b/macros.xml Wed Nov 27 12:35:23 2019 +0000 @@ -1,40 +1,46 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">1.11.4</token> - <token name="@GALAXY_TOOL_VERSION@">0.2.7</token> + <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 name="minoffset" type="float" label="minoffset" value="0.5" argument='--minoffset' + <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 name="maxoffset" type="float" label="maxoffset" value="0.5" argument='--maxoffset' + <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 name="ilim" type="float" value="0.05" argument='--ilim' + <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 name="iw_norm" type="select" label="Normalisation for isolation efficiency"> + <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 name="isotopes" type="select" label="Handling of isotopic peaks" > + <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> @@ -44,7 +50,7 @@ <when value="exclude_default"> </when> <when value="user"> - <param name="im" type="data" format="tabular" label="Isotope matrix" help=" + <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']. @@ -58,7 +64,7 @@ <xml name="camera_xcms"> - <param name="camera_xcms" type="select" label="Use CAMERA object or XCMS object from RData?" + <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> @@ -95,24 +101,23 @@ <when value="no"> </when> <when value="yes"> - <param type="data" name="grp_peaklist" label="grouped peaklist" + <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 name="@QL_SHRT@_dbPth_select" type="select" label="Input" help="@HELP@" > + <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 type="data" name="@QL_SHRT@_dbPth" label="@QL@ SQLite database" format="sqlite" help=""/> + <param argument="--@QL_SHRT@_dbPth" type="data" label="@QL@ SQLite database" format="sqlite" help=""/> </when> <when value="local_config"> </when> @@ -127,13 +132,13 @@ <section name="@QL_SHRT@_filters" title="Filters" expanded="False"> - <param name="@QL_SHRT@_ppmPrec" type="float" value="5" label="ppm error of the precursor for spectra"/> - <param name="@QL_SHRT@_ppmProd" type="float" value="10" label="ppm error of the product for spectra"/> + <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 name="@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/> + <param argument="--@QL_SHRT@_raThres" type="float" value = '2' label="Relative abundance threshold"/> </when> <when value="false"> </when> @@ -142,7 +147,7 @@ <conditional name="@QL_SHRT@_polarity_cond"> <param name="@QL_SHRT@_polarity_bool" type="boolean" label="Filter on polarity?" help="" /> <when value="true"> - <param name="@QL_SHRT@_polarity" type="select" label="Polarity" multiple="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> @@ -155,7 +160,7 @@ <conditional name="@QL_SHRT@_purity_cond"> <param name="@QL_SHRT@_purity_bool" type="boolean" label="Filter on precursor ion purity?"/> <when value="true"> - <param name="@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6" + <param argument="--@QL_SHRT@_purity" type="float" min="0" max="1" value="0.6" label="Precursor ion purity threshold"/> </when> <when value="false"> @@ -165,7 +170,7 @@ <conditional name="@QL_SHRT@_xcmsGroups_cond"> <param name="@QL_SHRT@_xcmsGroups_bool" type="boolean" label="Filter on XCMS groups ids?"/> <when value="true"> - <param name="@QL_SHRT@_xcmsGroups" type="text" value="" + <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'" /> @@ -178,7 +183,7 @@ <conditional name="@QL_SHRT@_pids_cond"> <param name="@QL_SHRT@_pids_bool" type="boolean" label="Filter on pids?"/> <when value="true"> - <param name="@QL_SHRT@_pids" type="text" value="" + <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'" /> @@ -193,9 +198,9 @@ label="Filter on retention time range?" help="Filter the spectra between two points of retention time range"/> <when value="true"> - <param name="@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)" + <param argument="--@QL_SHRT@_rtrangeMin" label="Minimum retention time range (seconds)" type="float" value="0" help=""/> - <param name="@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)" + <param argument="--@QL_SHRT@_rtrangeMax" label="Maximum retention time range (seconds)" type="float" value="3000" help=""/> </when> <when value="false"> @@ -209,7 +214,7 @@ label="Filter on accessions?" help="Filter on unique accessions IDs (e.g. from MassBank and MoNA)"/> <when value="true"> - <param name="@QL_SHRT@_accessions" type="text" value="" + <param argument="--@QL_SHRT@_accessions" type="text" value="" label="Spectra accessions" help="Comma seperated list of accessions)) e.g 'AC000001,BS001003,LIT00001'" /> @@ -223,7 +228,7 @@ <param name="@QL_SHRT@_sources_bool" type="boolean" label="Filter on sources?" help="" value="@SOURCES_SELECT@" /> <when value="true"> - <param name="@QL_SHRT@_sources" type="select" multiple="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: @@ -246,7 +251,7 @@ value="@INSTRUMENT_TYPES_SELECT@" label="Filter on instrument type?" help="" /> <when value="true"> - <param name="@QL_SHRT@_instrumentTypes" type="select" multiple="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> @@ -303,7 +308,7 @@ <option value="Quattro_QQQ" selected="true">Quattro_QQQ</option> <option value="none">None</option> </param> - <param name="@QL_SHRT@_instrumentTypesUser" type="text" value="" + <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> @@ -313,7 +318,7 @@ <conditional name="@QL_SHRT@_instruments_cond"> <param name="@QL_SHRT@_instruments_bool" type="boolean" label="Filter on instrument name?" help="" /> <when value="true"> - <param name="@QL_SHRT@_instruments" type="text" value="" + <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> @@ -327,7 +332,7 @@ <param name="@QL_SHRT@_spectraTypes_bool" type="boolean" label="Filter on spectral type?" help="" /> <when value="true"> - <param name="@QL_SHRT@_spectraTypes" type="select" multiple="true" label="Spectra type" > + <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> @@ -339,7 +344,7 @@ </when> </conditional> - <param name="@QL_SHRT@_spectraFilter" type="boolean" checked="true" + <param argument="--@QL_SHRT@_spectraFilter" type="boolean" checked="true" label="Ignore any peaks flagged in the spectra in previous stages?" help="" />