Commit 58406542 authored by Lucille Delisle's avatar Lucille Delisle
Browse files

use .gz as suggested by @mvdbeek

parent e9704f1e

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

+4 −4
Original line number Diff line number Diff line
@@ -476,10 +476,10 @@ 
    <datatype extension="protobuf3" type="galaxy.datatypes.binary:Binary" subclass="true" description="Protocol Buffers (Protobuf) is data format for serializing structured data." display_in_upload="true"/>

    <datatype extension="onnx" type="galaxy.datatypes.binary:Binary" subclass="true" description="ONNX (Open neural network exchange) is data format for storing and sharing machine learning and deep learning models." display_in_upload="true"/>

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

    <datatype extension="interval_tabix" type="galaxy.datatypes.interval:IntervalTabix" mimetype="application/octet-stream" />

    <datatype extension="juicer_medium_tabix" type="galaxy.datatypes.interval:JuicerMediumTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="bed_tabix" type="galaxy.datatypes.interval:BedTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="gff_tabix" type="galaxy.datatypes.interval:GffTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="interval_tabix.gz" type="galaxy.datatypes.interval:IntervalTabix" mimetype="application/octet-stream" />

    <datatype extension="juicer_medium_tabix.gz" type="galaxy.datatypes.interval:JuicerMediumTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="bed_tabix.gz" type="galaxy.datatypes.interval:BedTabix" mimetype="application/octet-stream" display_in_upload="true"/>

    <datatype extension="gff_tabix.gz" type="galaxy.datatypes.interval:GffTabix" mimetype="application/octet-stream" display_in_upload="true"/>

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

    <datatype extension="vcf_bgzip" type="galaxy.datatypes.tabular:VcfGz" display_in_upload="true">

      <display file="igv/vcf.xml"/>

lib/galaxy/datatypes/interval.py

+4 −4
Original line number Diff line number Diff line
@@ -1736,7 +1736,7 @@ class IntervalTabix(Interval): 
    As tabix is just a bgzip sorted for chr,start,end with an index

    """



    file_ext = "interval_tabix"

    file_ext = "interval_tabix.gz"

    edam_format = "format_3616"

    compressed = True

    compressed_format = "gzip"
@@ -1810,7 +1810,7 @@ class JuicerMediumTabix(IntervalTabix): 
    mapq = mapping quality score

    """



    file_ext = "juicer_medium_tabix"

    file_ext = "juicer_medium_tabix.gz"



    # The MetadataElements are readonly so the user cannot change them (as the index is generated only once)

    MetadataElement(name="chromCol", default=3, desc="Chrom column", param=metadata.ColumnParameter, readonly=True)
@@ -1823,7 +1823,7 @@ class BedTabix(IntervalTabix): 
    Class describing a tabix file built from a bed file

    """



    file_ext = "bed_tabix"

    file_ext = "bed_tabix.gz"





class GffTabix(IntervalTabix):
@@ -1831,7 +1831,7 @@ class GffTabix(IntervalTabix): 
    Class describing a tabix file built from a bed file

    """



    file_ext = "gff_tabix"

    file_ext = "gff_tabix.gz"



    # The MetadataElements are readonly so the user cannot change them (as the index is generated only once)

    MetadataElement(name="startCol", default=4, desc="Start column", param=metadata.ColumnParameter, readonly=True)