Mercurial > repos > tomnl > mspurity_createdatabase
comparison createDatabase.xml @ 3:7c0834ead235 draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e05cb49ba56d359fec34f132d1c9ace582e5b483-dirty
| author | tomnl |
|---|---|
| date | Tue, 18 Jun 2019 10:04:42 -0400 |
| parents | 52999a8b46fb |
| children | a3a969a82106 |
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| 2:52999a8b46fb | 3:7c0834ead235 |
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| 32 #end if | 32 #end if |
| 33 | 33 |
| 34 #if $eic | 34 #if $eic |
| 35 --eic | 35 --eic |
| 36 #end if | 36 #end if |
| 37 #if $raw_rt_columns | 37 |
| 38 --raw_rt_columns | |
| 39 #end if | |
| 40 #if $grp_peaklist_opt.grp_peaklist_opt=="yes" | 38 #if $grp_peaklist_opt.grp_peaklist_opt=="yes" |
| 41 --grp_peaklist=$grp_peaklist | 39 --grp_peaklist=$grp_peaklist |
| 42 #end if | 40 #end if |
| 43 | 41 |
| 44 ]]></command> | 42 ]]></command> |
| 45 <inputs> | 43 <inputs> |
| 46 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object" | 44 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object" |
| 47 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. | 45 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. |
| 48 Please specify which to use below" | 46 Please specify which to use below" |
| 49 format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/> | 47 format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/> |
| 50 <expand macro="camera_xcms" /> | 48 <expand macro="camera_xcms" /> |
| 51 <param type="data" name="pa" label="purityA object (frag4feature output)" format="rdata" | 49 <param type="data" name="pa" label="purityA object (frag4feature output)" format="rdata" |
| 52 help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/> | 50 help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/> |
| 53 <param name="eic" type="boolean" label="Include EIC data?" | 51 <param name="eic" type="boolean" label="Include EIC data?" |
| 54 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in | 52 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in |
| 55 the database. Note, this will take considerable time for large datasets and | 53 the database. Note, this will take considerable time for large datasets and |
| 56 the resulting SQLite database can be large"/> | 54 the resulting SQLite database can be large"/> |
| 57 <param name="raw_rt_columns" type="boolean" label="Use user defined Raw RT columns?" | |
| 58 help="Only use if the track_rt_raw tool has been used"/> | |
| 59 <expand macro="grp_peaklist" /> | 55 <expand macro="grp_peaklist" /> |
| 60 <expand macro="fileload" /> | 56 <expand macro="fileload" /> |
| 61 </inputs> | 57 </inputs> |
| 62 <outputs> | 58 <outputs> |
| 63 <data name="createDatabase_output_sqlite" format="sqlite" | 59 <data name="createDatabase_output_sqlite" format="sqlite" |