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Add deprecation warning for solexa, illumina quality encoding
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mvdbeek committed Jul 29, 2024
1 parent dd902c4 commit 68b9f64
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6 changes: 6 additions & 0 deletions lib/galaxy/config/sample/datatypes_conf.xml.sample
Original file line number Diff line number Diff line change
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</datatype>
<datatype extension="fastqsolexa" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true" description="Solexa variant of the FASTQ format: solexa+64" description_url="https://wiki.galaxyproject.org/Learn/Datatypes#FastqSolexa">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
<upload_warning>
Sequencing data produced since February 2011 is generally using Sanger encoding. Please consider selecting fastqsanger${auto_compressed_type} instead.
</upload_warning>
</datatype>
<datatype extension="fastqcssanger" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true" description="sequence in in color space phred scored quality values 0:93 represented by ASCII 33:126">
<upload_warning>
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</datatype>
<datatype extension="fastqillumina" auto_compressed_types="gz,bz2" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true" description="Sanger variant of the FASTQ format: phred+64">
<converter file="fastq_to_fqtoc.xml" target_datatype="fqtoc"/>
<upload_warning>
Sequencing data produced since February 2011 is generally using Sanger encoding. Please consider selecting fastqsanger${auto_compressed_type} instead.
</upload_warning>
</datatype>
<datatype extension="fqtoc" type="galaxy.datatypes.sequence:SequenceSplitLocations" display_in_upload="true"/>
<datatype extension="eland" type="galaxy.datatypes.tabular:Eland" display_in_upload="true"/>
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