Unverified Commit 68b9f64a authored by mvdbeek's avatar mvdbeek
Browse files

Add deprecation warning for solexa, illumina quality encoding

parent dd902c4d

lib/galaxy/config/sample/datatypes_conf.xml.sample

+6 −0
Original line number Diff line number Diff line
@@ -152,6 +152,9 @@ 
    </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>
@@ -161,6 +164,9 @@ 
    </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"/>