Mercurial > repos > computational-metabolomics > mspurity_createdatabase
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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author | computational-metabolomics |
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date | Thu, 13 Jun 2024 11:39:21 +0000 |
parents | 2f71b3495221 |
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<tool id="mspurity_createdatabase" name="msPurity.createDatabase" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@"> <description>Create and SQLite database of an LC-MS(/MS) experiment</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ Rscript '$__tool_directory__/createDatabase.R' --outDir=. --xset_xa='$xset_xa' --pa='$pa' --xcms_camera_option=$camera_xcms --cores=\${GALAXY_SLOTS:-4} #if $file_load_conditional.file_load_select=="yes" --mzML_files=' #for $i in $file_load_conditional.input $i, #end for ' --galaxy_names=' #for $i in $file_load_conditional.input $i.name, #end for ' #end if #if $eic --eic #end if #if $grp_peaklist_opt.grp_peaklist_opt=="yes" --grpPeaklist='$grp_peaklist' #end if ]]></command> <inputs> <param argument="--xset_xa" type="data" label="xcmsSet or CAMERA object" help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. Please specify which to use below" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/> <expand macro="camera_xcms" /> <param argument="--pa" type="data" label="purityA object (frag4feature output)" format="rdata" help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/> <param argument="--eic" type="boolean" label="Include EIC data?" help="The Extracted Ion Chromatogram can be calculated for each peak and stored in the database. Note, this will take considerable time for large datasets and the resulting SQLite database can be large"/> <expand macro="grp_peaklist" /> <expand macro="fileload" /> </inputs> <outputs> <data name="createDatabase_output_sqlite" format="sqlite" label="${tool.name} on ${on_string}: LC-MS(/MS) data SQLite db" from_work_dir="createDatabase_output.sqlite" /> </outputs> <tests> <test> <conditional name="file_load_conditional"> <param name="file_load_select" value="yes"/> <param name="input" > <collection type="list"> <element name="LCMS_1.mzML" value="LCMS_1.mzML"/> <element name="LCMS_2.mzML" value="LCMS_2.mzML"/> <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/> <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/> </collection> </param> </conditional> <param name="camera_xcms" value="xcms"/> <param name="xset_xa" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/> <param name="pa" value="averageFragSpectra_output_all.RData"/> <output name="createDatabase_output_sqlite" value="createDatabase_output.sqlite" ftype="sqlite" compare="sim_size"/> </test> <test> <conditional name="file_load_conditional"> <param name="file_load_select" value="yes"/> <param name="input" > <collection type="list"> <element name="LCMS_1.mzML" value="LCMS_1.mzML"/> <element name="LCMS_2.mzML" value="LCMS_2.mzML"/> <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/> <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/> </collection> </param> </conditional> <param name="camera_xcms" value="xcms"/> <param name="eic" value="true"/> <param name="xset_xa" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/> <param name="pa" value="averageFragSpectra_output_all.RData"/> <output name="createDatabase_output_sqlite" value="createDatabase_output_eic.sqlite" ftype="sqlite" compare="sim_size"/> </test> </tests> <help><![CDATA[ ============================================================= Create SQLite database for LC-MS(/MS) dataset ============================================================= ** General ** Create and SQLite database of an LC-MS(/MS) experiment (replaces the create_database function). Schema details can be found [here](https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html). **Example LC-MS/MS processing workflow** * Purity assessments + (mzML files) -> purityA -> (pa) * XCMS processing + (mzML files) -> xcms.xcmsSet -> xcms.merge -> xcms.group -> xcms.retcor -> xcms.group -> (xset) * Fragmentation processing + (xset, pa) -> frag4feature -> filterFragSpectra -> averageAllFragSpectra -> **createDatabase** -> spectralMatching -> (sqlite spectral database) ----------- Output ----------- * lcms_sqlite: An SQLite database of the LC-MS(/MS) data (including fragmentation scans) ]]></help> <expand macro="citations" /> </tool>