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comparison create_sqlite_db.xml @ 13:4acad02faf32 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e6935a8c6a3da23f47a753ab5a8159fa9d165535
author tomnl
date Fri, 11 May 2018 06:08:10 -0400
parents c59965822dc8
children 69d5cb5a8e90
comparison
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12:225009d1f603 13:4acad02faf32
1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.6"> 1 <tool id="create_sqlite_db" name="create_sqlite_db" version="0.0.9">
2 <description> 2 <description>
3 Create SQLite database of an XCMS-CAMERA dataset 3 Create SQLite database of an XCMS-CAMERA dataset
4 </description> 4 </description>
5 5
6 6
66 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object" 66 <param type="data" name="xset_xa" label="xcmsSet or CAMERA object"
67 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. Please 67 help="Either xcmsSet object saved as 'xset' or CAMERA 'xa' object in an RData file. Please
68 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"/> 68 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"/>
69 <expand macro="camera_xcms" /> 69 <expand macro="camera_xcms" />
70 70
71 <param type="data" name="pa" label="purityA object" format="rdata" 71 <param type="data" name="pa" label="purityA object (frag4feature output)" format="rdata"
72 help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/> 72 help="purityA object saved as 'pa' in a RData file (output from frag4feature)"/>
73 73
74 <param name="eic" type="boolean" label="Include EIC data?" 74 <param name="eic" type="boolean" label="Include EIC data?"
75 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in 75 help="The Extracted Ion Chromatogram can be calculated for each peak and stored in
76 the database. Note, this will take considerable time for large datasets and 76 the database. Note, this will take considerable time for large datasets and
77 the resulting SQLite database can be large"/> 77 the resulting SQLite database can be large"/>
146 </param> 146 </param>
147 </conditional> 147 </conditional>
148 <param name="camera_xcms" value="xcms"/> 148 <param name="camera_xcms" value="xcms"/>
149 <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/> 149 <param name="xset_xa" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
150 <param name="pa" value="frag4feature.rdata"/> 150 <param name="pa" value="frag4feature.rdata"/>
151
151 <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" > 152 <output name="cpeakgroup_msms" value="cpeakgroup_msms.tsv" >
153
152 154
153 </output> 155 </output>
154 </test> 156 </test>
155 </tests> 157 </tests>
156 158