| Previous changeset 18:d1ea609e57d4 (2015-05-20) Next changeset 20:300fc3aa6954 (2015-06-04) |
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Commit message:
planemo upload for repository https://github.com/iracooke/proteomics-datatypes commit a71820c91d9d7629415a27526bbf700800d12f3f |
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modified:
datatypes_conf.xml proteomics.py |
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| diff -r d1ea609e57d4 -r e5551a35e508 datatypes_conf.xml --- a/datatypes_conf.xml Wed May 20 01:39:39 2015 -0400 +++ b/datatypes_conf.xml Wed Jun 03 18:24:50 2015 -0400 |
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| @@ -46,7 +46,12 @@ <datatype extension="msp" type="galaxy.datatypes.proteomics:Msp" display_in_upload="true" /> <datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true" /> <datatype extension="hlf" type="galaxy.datatypes.proteomics:XHunterAslFormat" mimetype="application/octet-stream" display_in_upload="true" /> + <datatype extension="splib" type="galaxy.datatypes.proteomics:SPLibNoIndex" display_in_upload="true" /> <datatype extension="splib" type="galaxy.datatypes.proteomics:SPLib" display_in_upload="true" /> + <datatype extension="sf3" type="galaxy.datatypes.proteomics:Sf3" display_in_upload="true" /> + <datatype extension="searchgui_zip" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> + <datatype extension="peptideshaker_zip" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> + </registration> <sniffers> <sniffer type="galaxy.datatypes.proteomics:MzML"/> |
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| diff -r d1ea609e57d4 -r e5551a35e508 proteomics.py --- a/proteomics.py Wed May 20 01:39:39 2015 -0400 +++ b/proteomics.py Wed Jun 03 18:24:50 2015 -0400 |
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| @@ -285,6 +285,19 @@ with open(filename, 'r') as contents: return Msp.next_line_starts_with(contents, "Name:") and Msp.next_line_starts_with(contents, "MW:") +class SPLibNoIndex( Text ): + """SPlib without index file """ + file_ext = "splib" + + def set_peek( self, dataset, is_multi_byte=False ): + """Set the peek and blurb text""" + if not dataset.dataset.purged: + dataset.peek = data.get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) + dataset.blurb = 'Spectral Library without index files' + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + class SPLib( Msp ): """SpectraST Spectral Library. Closely related to msp format""" @@ -378,3 +391,13 @@ if hasattr(Binary, 'register_unsniffable_binary_ext'): Binary.register_unsniffable_binary_ext('hlf') + + +class Sf3(Binary): + """Class describing a Scaffold SF3 files""" + file_ext = "sf3" + +if hasattr(Binary, 'register_unsniffable_binary_ext'): + Binary.register_unsniffable_binary_ext('sf3') + + |