Unverified Commit 7765deac authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
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Merge pull request #18612 from mvdbeek/more_datatype_deprecation_warnings 

[24.1] More datatype deprecation warnings
parents 257d9dc4 68b9f64a

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

+11 −1
Original line number Diff line number Diff line
@@ -114,7 +114,11 @@ 
    <datatype extension="customtrack" type="galaxy.datatypes.interval:CustomTrack"/>

    <datatype extension="bowtie_color_index" type="galaxy.datatypes.ngsindex:BowtieColorIndex" mimetype="text/html" display_in_upload="false"/>

    <datatype extension="bowtie_base_index" type="galaxy.datatypes.ngsindex:BowtieBaseIndex" mimetype="text/html" display_in_upload="false"/>

    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true"/>

    <datatype extension="csfasta" type="galaxy.datatypes.sequence:csFasta" display_in_upload="true">

        <upload_warning>

          SOLID Color-Space sequence data is a rare data type. Consider selecting fasta instead.

        </upload_warning>

    </datatype>

    <datatype extension="data" type="galaxy.datatypes.data:Data" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>

    <datatype extension="gz" type="galaxy.datatypes.binary:Binary" subclass="true"/>

    <datatype extension="binary" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" max_optional_metadata_filesize="1048576"/>
@@ -148,6 +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>
@@ -157,6 +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"/>