Mercurial > repos > tomnl > mspurity_spectralmatching
diff spectralMatching.xml @ 15:945e73261fbb draft default tip
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc
| author | tomnl |
|---|---|
| date | Wed, 27 Nov 2019 12:30:07 +0000 |
| parents | 499c26566a7a |
| children |
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--- a/spectralMatching.xml Fri Sep 27 09:10:22 2019 -0400 +++ b/spectralMatching.xml Wed Nov 27 12:30:07 2019 +0000 @@ -2,20 +2,12 @@ <description> Perform spectral matching to MS/MS spectral libraries </description> - <macros> <import>macros.xml</import> </macros> - - <expand macro="requirements"> - </expand> - - - <stdio> - <exit_code range="1:" /> - </stdio> - <command interpreter="Rscript"><![CDATA[ - spectralMatching.R + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$__tool_directory__/spectralMatching.R' --outDir=. --cores=\${GALAXY_SLOTS:-4} @@ -103,30 +95,30 @@ #if $Query.q_filters.q_sources_cond.q_sources_bool --q_sources=$Query.q_filters.q_sources_cond.q_sources - --q_sourcesUser="$Query.q_filters.q_sources_cond.q_sourcesUser" + --q_sourcesUser='$Query.q_filters.q_sources_cond.q_sourcesUser' #end if #if $Library.l_filters.l_sources_cond.l_sources_bool --l_sources=$Library.l_filters.l_sources_cond.l_sources - --l_sourcesUser="$Library.l_filters.l_sources_cond.l_sourcesUser" + --l_sourcesUser='$Library.l_filters.l_sources_cond.l_sourcesUser' #end if #if $Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes_bool - --q_instrumentTypes="$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes" - --q_instrumentTypesUser="$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser" + --q_instrumentTypes='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypes' + --q_instrumentTypesUser='$Query.q_filters.q_instrumentTypes_cond.q_instrumentTypesUser' #end if #if $Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes_bool - --l_instrumentTypes="$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes" - --l_instrumentTypesUser="$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser" + --l_instrumentTypes='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypes' + --l_instrumentTypesUser='$Library.l_filters.l_instrumentTypes_cond.l_instrumentTypesUser' #end if #if $Query.q_filters.q_instruments_cond.q_instruments_bool - --q_instruments="$Query.q_filters.q_instruments_cond.q_instruments" + --q_instruments=$Query.q_filters.q_instruments_cond.q_instruments #end if #if $Library.l_filters.l_instruments_cond.l_instruments_bool - --l_instruments="$Library.l_filters.l_instruments_cond.l_instruments" + --l_instruments='$Library.l_filters.l_instruments_cond.l_instruments' #end if #if $Query.q_filters.q_spectraTypes_cond.q_spectraTypes_bool @@ -163,100 +155,74 @@ --usePrecursors #end if - - ]]></command> <inputs> - - - - <section name="Query" title="Query spectra input and filters" expanded="True"> - <expand macro="sm_input" ql='Query' ql_shrt = "q" user="True" mspuritydatalib="False" msp="False" + <section name="Query" title="Query spectra input and filters" expanded="True"> + <expand macro="sm_input" ql="Query" ql_shrt = "q" user="True" mspuritydatalib="False" msp="False" help="Query SQLite database - in the standard XCMS msPurity workflow - the output - of msPurity.createDatabase should be used here. However any SQLite database - following the schema of as https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/> - <expand macro="filters" ql="Query" ql_shrt="q"/> - </section> - - <section name="Library" title="Library spectra input and filters" expanded="True"> - <expand macro="sm_input" ql='Library' ql_shrt = "l" user="False" mspuritydatalib="True" msp="False" + of msPurity.createDatabase should be used here. However any SQLite database + following the schema of as https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/> + <expand macro="filters" ql="Query" ql_shrt="q"/> + </section> + <section name="Library" title="Library spectra input and filters" expanded="True"> + <expand macro="sm_input" ql="Library" ql_shrt = "l" user="False" mspuritydatalib="True" msp="False" help="Library SQLite database - in the standard XCMS msPurity workflow - a default - database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite - database following the schema of https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/> - <expand macro="filters" ql="Library" ql_shrt="l"/> - </section> - - <section name="General" title="General arguments" expanded="False"> - <conditional name="rttol_cond"> + database of MassBank, HMDB, LipidBlast and GNPS is used. However any SQLite + database following the schema of https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html can be used as input"/> + <expand macro="filters" ql="Library" ql_shrt="l"/> + </section> + <section name="General" title="General arguments" expanded="False"> + <conditional name="rttol_cond"> <param name="rttol_bool" type="boolean" label="Filter on retention time match?" - help="" /> - <when value="true"> - <param name="rttol" type="float" value="30" min="0" - label="Retention time tolerance (seconds)" - help="Retention time tolerance in seconds to match precursors"/> - </when> - <when value="false"> - </when> - </conditional> - - - <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?" - help="If True, spectra will be filtered by similarity of precursors based on - the library and query ppm defined tolerance" /> - - <param name="raW" label="Weighting for relative abundance" - type="float" value="0.5" - help="Relative abundance weight for spectra (default to 0.5 as determined by - massbank for ESI data)"/> - - <param name="mzW" label="Weighting for mz" - type="float" value="2" - help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/> - - <conditional name="updateDb_cond"> + help="" /> + <when value="true"> + <param name="rttol" type="float" value="30" min="0" + label="Retention time tolerance (seconds)" + help="Retention time tolerance in seconds to match precursors"/> + </when> + <when value="false"/> + </conditional> + <param name="usePrecursors" type="boolean" checked="true" label="Filter on matching precursors?" + help="If True, spectra will be filtered by similarity of precursors based on + the library and query ppm defined tolerance" /> + <param name="raW" label="Weighting for relative abundance" type="float" value="0.5" + help="Relative abundance weight for spectra (default to 0.5 as determined by + massbank for ESI data)"/> + <param name="mzW" label="Weighting for mz" type="float" min="0" value="2" + help="mz weight for spectra (default to 2 as determined by massbank for ESI data)"/> + <conditional name="updateDb_cond"> <param name="updateDb" type="boolean" checked="true" - label="Update database with results?" help="" /> - <when value="true"> - <param name="copyDb" type="boolean" checked="true" - label="Make a copy of the database?" - help="A copy will be made of the input SQLite target database and the - results will be added to this copy. When False, the input SQLite - database will be updated with the matching results. Use False if - you want to reduce storage space being used."/> - </when> - <when value="false"> - </when> - </conditional> - - - + label="Update database with results?" help="" /> + <when value="true"> + <param name="copyDb" type="boolean" checked="true" + label="Make a copy of the database?" + help="A copy will be made of the input SQLite target database and the + results will be added to this copy. When False, the input SQLite + database will be updated with the matching results. Use False if + you want to reduce storage space being used."/> + </when> + <when value="false"/> + </conditional> </section> - - - - </inputs> <outputs> <data name="sqlite_results" format="sqlite" label="${tool.name} on ${on_string}: SQLite results" - from_work_dir="db_with_spectral_matching.sqlite" > + from_work_dir="db_with_spectral_matching.sqlite" > <filter>create_new_database is True</filter> </data> <data name="matches" format="tsv" label="${tool.name} on ${on_string}: matches" - from_work_dir="matched_results.tsv" > + from_work_dir="matched_results.tsv" > <filter>spectra_type_q == "scans"</filter> </data> <data name="xcms_matches" format="tsv" label="${tool.name} on ${on_string}: XCMS matches" - from_work_dir="xcms_matched_results.tsv" /> + from_work_dir="xcms_matched_results.tsv" /> </outputs> <tests> <test> - - <param name="q_dbPth" value="createDatabase_output.sqlite" /> - <param name="l_dbPth_select" value="userdb" /> + <param name="l_dbPth_select" value="userdb" /> <param name="l_dbPth" value="PR100037.sqlite" /> - <param name="q_xcmsGroups_bool" value="true" /> <param name="l_accessions_bool" value="true" /> <param name="q_xcmsGroups" value="14" /> @@ -268,24 +234,18 @@ <test> <param name="l_instrumentTypes_bool" value="true" /> <param name="q_dbPth" value="createDatabase_output.sqlite" /> - <param name="l_dbPth_select" value="userdb" /> + <param name="l_dbPth_select" value="userdb" /> <param name="l_dbPth" value="PR100037.sqlite" /> - <param name="q_xcmsGroups_bool" value="true" /> <param name="l_accessions_bool" value="true" /> <param name="q_xcmsGroups" value="14" /> <param name="l_accessions" value="PR100037" /> - <output name="xcms_matches" file="spectralMatching_matched_results_instrumentTypes.tsv" /> <output name="matches" file="spectralMatching_xcms_matched_results_instrumentTypes.tsv" /> <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching_instrumentTypes.sqlite" ftype="sqlite" compare="sim_size"/> </test> - - </tests> - - <help><![CDATA[ ============================================================= @@ -407,5 +367,5 @@ ]]></help> -<expand macro="citations"> </expand> + <expand macro="citations"> </expand> </tool>