Mercurial > repos > tomnl > mspurity_dimspredictpuritysingle
diff macros.xml @ 10:1ce857d74106 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
| author | tomnl |
|---|---|
| date | Thu, 27 Jun 2019 12:40:06 -0400 |
| parents | c874652f3029 |
| children | a90832e6acb2 |
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--- a/macros.xml Tue Jun 25 12:44:13 2019 -0400 +++ b/macros.xml Thu Jun 27 12:40:06 2019 -0400 @@ -1,11 +1,16 @@ <?xml version="1.0"?> <macros> + <token name="@TOOL_VERSION@">1.11.3</token> + <token name="@GALAXY_TOOL_VERSION@">0.2.5</token> + <xml name="requirements"> <requirements> - <requirement type="package" version="1.11.2" >bioconductor-mspurity</requirement> + <requirement type="package" version="@TOOL_VERSION@" >bioconductor-mspurity</requirement> <yield /> </requirements> </xml> + + <xml name="offsets"> <param name="minoffset" type="float" label="minoffset" value="0.5" argument='--minoffset' help="Offset to the 'left' for the precursor range e.g. if precursor of interest is @@ -96,7 +101,7 @@ </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=""> @@ -105,28 +110,28 @@ <option value="userdb" selected="@USER@" >SQLite database of (LC)-MS/MS data</option> <option value="msPurityData" selected="@MSPURITYDATALIB@" >Prepared database of MassBank, HMDB, LipidBlast and GNPS</option> <option value="msp" >MSP file (SQLite database will be created using using msp2db)</option> - </param> + </param> <when value="userdb"> <param type="data" name="@QL_SHRT@_dbPth" label="@QL@ SQLite database" format="sqlite" help=""/> </when> <when value="msp"> <param type="data" name="@QL_SHRT@_msp" label="@QL@ MSP file" format="msp" help=""/> </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 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"/> - + <conditional name="@QL_SHRT@_raThres_cond"> <param name="@QL_SHRT@_raThres_bool" type="boolean" label="Filter on relative abundance threshold?"/> <when value="true"> @@ -135,7 +140,7 @@ <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"> @@ -148,7 +153,7 @@ <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"> @@ -158,35 +163,35 @@ <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 name="@QL_SHRT@_xcmsGroups" type="text" value="" - label="XCMS group ids of spectra" + 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 name="@QL_SHRT@_pids" type="text" value="" - label="pids of spectra (correspond to column 'pid; in s_peak_meta)" + 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" + <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"> @@ -198,32 +203,32 @@ <when value="false"> </when> </conditional> - - - + + + <conditional name="@QL_SHRT@_accessions_cond"> - <param name="@QL_SHRT@_accessions_bool" type="boolean" + <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 name="@QL_SHRT@_accessions" type="text" value="" - label="Spectra accessions" + 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" + <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" - 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: + 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> @@ -239,7 +244,7 @@ </when> </conditional> <conditional name="@QL_SHRT@_instrumentTypes_cond"> - <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean" + <param name="@QL_SHRT@_instrumentTypes_bool" type="boolean" value="@INSTRUMENT_TYPES_SELECT@" label="Filter on instrument type?" help="" /> <when value="true"> @@ -278,7 +283,7 @@ <option value="none">None</option> </param> <param name="@QL_SHRT@_instrumentTypesUser" type="text" value="" - help="Types of the instruments to be included in the search. Use a comma to + 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"> @@ -288,17 +293,17 @@ <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="" - help="Known instrument names to filter on. Use a comma to + 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?" + <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" > @@ -314,14 +319,14 @@ </conditional> <param name="@QL_SHRT@_spectraFilter" type="boolean" checked="true" - label="Ignore any peaks flagged in the spectra in previous stages?" + label="Ignore any peaks flagged in the spectra in previous stages?" help="" /> - + </section> </xml> - + - + <xml name="citations"> <citations>