Mercurial > repos > lecorguille > rdata_xcms_datatypes
changeset 1:544f6d2329ac draft default tip
planemo upload commit 9f72e947d9c241d11221cad561f3525d27231857
| author | lecorguille |
|---|---|
| date | Wed, 19 Sep 2018 02:50:28 -0400 |
| parents | d64562a4ebb3 |
| children | |
| files | datatypes_conf.xml rdata_xcms_datatype.py |
| diffstat | 2 files changed, 28 insertions(+), 25 deletions(-) [+] |
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--- a/datatypes_conf.xml Fri Aug 07 10:44:06 2015 -0400 +++ b/datatypes_conf.xml Wed Sep 19 02:50:28 2018 -0400 @@ -4,10 +4,10 @@ <datatype_file name="rdata_xcms_datatype.py"/> </datatype_files> <registration> - <datatype extension="rdata" type="galaxy.datatypes.binary:Binary" mimetype="application/x-gzip" subclass="true" display_in_upload="true" /> - <datatype extension="rdata.xcms.raw" type="galaxy.datatypes.rdata_xcms_datatype:RdataXcmsRaw" mimetype="application/x-gzip" subclass="true" display_in_upload="true" /> + <datatype extension="rdata.msnbase.raw" type="galaxy.datatypes.rdata_xcms_datatype:RdataMsnbaseRaw" mimetype="application/x-gzip" subclass="true" display_in_upload="true" /> + <datatype extension="rdata.xcms.findchrompeaks" type="galaxy.datatypes.rdata_xcms_datatype:RdataXcmsFindChromPeaks" mimetype="application/x-gzip" subclass="true" display_in_upload="true" /> <datatype extension="rdata.xcms.group" type="galaxy.datatypes.rdata_xcms_datatype:RdataXcmsGroup" mimetype="application/x-gzip" subclass="true" display_in_upload="true" /> - <datatype extension="rdata.xcms.retcor" type="galaxy.datatypes.rdata_xcms_datatype:RdataXcmsRetcor" mimetype="application/x-gzip" subclass="true" display_in_upload="true" /> + <datatype extension="rdata.xcms.retcor" type="galaxy.datatypes.rdata_xcms_datatype:RdataXcmsRetcor" mimetype="application/x-gzip" subclass="true" display_in_upload="true" /> <datatype extension="rdata.xcms.fillpeaks" type="galaxy.datatypes.rdata_xcms_datatype:RdataXcmsFillpeaks" mimetype="application/x-gzip" subclass="true" display_in_upload="true" /> </registration> </datatypes>
--- a/rdata_xcms_datatype.py Fri Aug 07 10:44:06 2015 -0400 +++ b/rdata_xcms_datatype.py Wed Sep 19 02:50:28 2018 -0400 @@ -9,36 +9,39 @@ import os,os.path,re from galaxy.datatypes.data import * from galaxy.datatypes.sniff import * -from galaxy.datatypes.binary import * +from galaxy.datatypes.binary import * log = logging.getLogger(__name__) - + + +class RdataMsnbaseRaw( RData ): + file_ext = "rdata.msnbase.raw" + blurb = "Output of MSnbase.readMSData\nInput of xcms.findChromPeaks" + + #TODO: sniff -class RdataXcmsRaw( Binary ): - file_ext = "rdata.xcms.raw" - blurb = "Output of xcms.xcmsSet\nInput of xcms.group and xcms.retcor" - +class RdataXcmsFindChromPeaks( RData ): + file_ext = "rdata.xcms.findchrompeaks" + blurb = "Output of xcms.findChromPeaks\nInput of xcms.groupChromPeaks and xcms.adjustRtime" + + #TODO: sniff + +class RdataXcmsGroup( RData ): + file_ext = "rdata.xcms.group" + blurb = "Output of xcms.groupChromPeaks\nInput of xcms.groupChromPeaks, xcms.adjustRtime, xcms.fillChromPeaks and camera.annotate" + #TODO: sniff -class RdataXcmsGroup( Binary ): - file_ext = "rdata.xcms.group" - blurb = "Output of xcms.group\nInput of xcms.group, xcms.retcor and xcms.fillpeaks" - +class RdataXcmsRetcor( RData ): + file_ext = "rdata.xcms.retcor" + blurb = "Output of xcms.adjustRtime\nInput of xcms.groupChromPeaks" + #TODO: sniff -class RdataXcmsRetcor( Binary ): - file_ext = "rdata.xcms.retcor" - blurb = "Output of xcms.retcor\nInput of xcms.group" - - #TODO: sniff - +class RdataXcmsFillpeaks( RData ): + file_ext = "rdata.xcms.fillpeaks" + blurb = "Output of xcms.fillChromPeaks\nInput of camera.annotate" -class RdataXcmsFillpeaks( Binary ): - file_ext = "rdata.xcms.fillpeaks" - blurb = "Output of xcms.fillpeaks\nInput of camera.annotate" - #TODO: sniff - -