comparison spectralMatching.xml @ 6:fecfe8c80e25 draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"

5:829af6fecd96

            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" value="PR100037.sqlite" />
            <param name="q_xcmsGroups_bool" value="true" />
            <param name="l_accessions_bool" value="true" />
            <param name="q_xcmsGroups" value="14" />

            <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/>
        </test>
        <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" value="PR100037.sqlite" />
            <param name="q_xcmsGroups_bool" value="true" />
            <param name="l_accessions_bool" value="true" />
            <param name="q_xcmsGroups" value="14" />

All matched results from the query spectra to the library spectra. Contains the same as above
without the XCMS details. This table is useful to observe spectral matching results
for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features.


.. _spectral_database_schema: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-datatabase-schema.html
.. _larger_database: https://github.com/computational-metabolomics/msp2db/releases
.. _msp2db: https://github.com/computational-metabolomics/msp2db/releases
.. _msPurity_spectral_matching_vignette: https://bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html

    ]]></help>

	<expand macro="citations">     </expand>
</tool>

6:fecfe8c80e25

            from_work_dir="xcms_matched_results.tsv" />
    </outputs>
    <tests>
        <test>
            <param name="q_dbPth" value="createDatabase_output.sqlite" />
            <param name="q_spectraTypes_bool" value="true" />
            <param name="q_spectraTypes" value="inter,av_all" />
	        <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" />

            <output name="sqlite_results" value="spectralMatching_db_with_spectral_matching.sqlite" ftype="sqlite" compare="sim_size"/>
        </test>
        <test>
            <param name="l_instrumentTypes_bool" value="true" />
            <param name="q_dbPth" value="createDatabase_output.sqlite" />
            <param name="q_spectraTypes_bool" value="true" />
            <param name="q_spectraTypes" value="inter,av_all" />
	    	<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" />

All matched results from the query spectra to the library spectra. Contains the same as above
without the XCMS details. This table is useful to observe spectral matching results
for all MS/MS spectra irrespective of if they are linked to XCMS MS1 features.


.. _spectral_database_schema: https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-spectral-database-vignette.html
.. _larger_database: https://github.com/computational-metabolomics/msp2db/releases
.. _msp2db: https://github.com/computational-metabolomics/msp2db/releases
.. _msPurity_spectral_matching_vignette: https://www.bioconductor.org/packages/release/bioc/vignettes/msPurity/inst/doc/msPurity-lcmsms-data-processing-and-spectral-matching-vignette.html

    ]]></help>

	<expand macro="citations">     </expand>
</tool>