comparison create_sqlite_db.xml @ 13:4acad02faf32 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535

12:225009d1f603

<tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.6">
    <description>
        Create SQLite database of an XCMS-CAMERA dataset
    </description>

        <param type="data" name="xset_xa" 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 type="data" name="pa" label="purityA object" format="rdata"
               help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/>

	<param name="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"/>

                </param>
            </conditional>
	    <param name="camera_xcms" value="xcms"/>
            <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
            <param name="pa" value="frag4feature.rdata"/>
            <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
                 
            </output>
        </test>
    </tests>
    

13:4acad02faf32

<tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.9">
    <description>
        Create SQLite database of an XCMS-CAMERA dataset
    </description>

        <param type="data" name="xset_xa" 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 type="data" name="pa" label="purityA object (frag4feature output)" format="rdata"
               help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/>

	<param name="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"/>

                </param>
            </conditional>
	    <param name="camera_xcms" value="xcms"/>
            <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
            <param name="pa" value="frag4feature.rdata"/>
           
            <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
            
                 
            </output>
        </test>
    </tests>