Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[18.01] Rename datatype extension 'bam_native' to 'unsorted.bam'. #5674

Merged
merged 2 commits into from
Mar 12, 2018
Merged

[18.01] Rename datatype extension 'bam_native' to 'unsorted.bam'. #5674

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
2db95b4
Rename datatype extension 'bam_native' to 'unsorted.bam'.
jmchilton Mar 12, 2018
9c0c8ee
Mention self.current_pr in release notes.
jmchilton Mar 12, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions config/datatypes_conf.xml.sample
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
</datatype>
<datatype extension="qname_sorted.bam" type="galaxy.datatypes.binary:BamQuerynameSorted" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted by queryname." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
</datatype>
<datatype extension="bam_native" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<datatype extension="unsorted.bam" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
Expand Down Expand Up @@ -297,7 +297,7 @@
<datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
<datatype extension="roadmaps" type="galaxy.datatypes.assembly:Roadmaps" display_in_upload="false"/>
<datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
<converter file="sam_to_bam_native.xml" target_datatype="bam_native"/>
<converter file="sam_to_unsorted_bam.xml" target_datatype="unsorted.bam"/>
<converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
<converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
Expand Down
2 changes: 1 addition & 1 deletion doc/source/releases/18.01_announce.rst
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,7 @@ Highlights

- ``qname_sorted.bam``, that ensures that the file is queryname sorted (e.g. ``SO:queryname``);
- ``qname_input_sorted.bam``, that can be used to describe the output of aligners which generally keep mate pairs adjacent
- ``native_bam``, that makes no assumptions about the sort order of the file.
- ``unsorted.bam``, that makes no assumptions about the sort order of the file.

A huge thanks goes out to `@bgruening <https://github.com/bgruening>`__ and `@mvdbeek <https://github.com/mvdbeek>`__ who
implemented these datatypes.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Maybe also reference this PR below.

Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/datatypes/binary.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -192,7 +192,7 @@ class BamNative(Binary):
"""Class describing a BAM binary file that is not necessarily sorted"""
edam_format = "format_2572"
edam_data = "data_0863"
file_ext = "bam_native"
file_ext = "unsorted.bam"
sort_flag = None

MetadataElement(name="bam_index", desc="BAM Index File", param=metadata.FileParameter, file_ext="bai", readonly=True, no_value=None, visible=False, optional=True)
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@
> temp.bg && bedGraphToBigWig temp.bg '$chromInfo' '$output']]>
</command>
<inputs>
<param format="bam,bam_native" name="input" type="data" label="Choose BAM file"/>
<param format="bam,unsorted.bam" name="input" type="data" label="Choose BAM file"/>
</inputs>
<outputs>
<data format="bigwig" name="output"/>
Expand Down
4 changes: 2 additions & 2 deletions ...atatypes/converters/sam_to_bam_native.xml → ...atypes/converters/sam_to_unsorted_bam.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="CONVERTER_sam_to_bam_native" name="Convert SAM to BAM native - without sorting" version="1.0.0" profile="18.01">
<tool id="CONVERTER_sam_to_unsorted_bam" name="Convert SAM to BAM without sorting" version="1.0.0" profile="18.01">
<requirements>
<requirement type="package" version="1.6">samtools</requirement>
</requirements>
Expand All @@ -15,7 +15,7 @@
<param name="input" type="data" format="sam" label="SAM file"/>
</inputs>
<outputs>
<data name="output" format="bam_native"/>
<data name="output" format="unsorted.bam"/>
</outputs>
<help>
</help>
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
]]>
</command>
<inputs>
<param format="sam,bam_native,qname_sorted.bam" name="input" type="data" label="Choose a BAM native or queryname sortedfile"/>
<param format="sam,unsorted.bam,qname_sorted.bam" name="input" type="data" label="Choose a BAM native or queryname sortedfile"/>
</inputs>
<outputs>
<data format="bam" name="output"/>
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
]]>
</command>
<inputs>
<param format="sam,bam_native" name="input" type="data" label="Choose a BAM native or queryname sortedfile"/>
<param format="sam,unsorted.bam" name="input" type="data" label="Choose a BAM native or queryname sortedfile"/>
</inputs>
<outputs>
<data format="qname_sorted.bam" name="output"/>
Expand Down
2 changes: 1 addition & 1 deletion lib/galaxy/datatypes/sniff.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -337,7 +337,7 @@ def guess_ext(fname, sniff_order):
'bam'
>>> fname = get_test_fname('3unsorted.bam')
>>> guess_ext(fname, sniff_order)
'bam_native'
'unsorted.bam'
>>> fname = get_test_fname('test.idpDB')
>>> guess_ext(fname, sniff_order)
'idpdb'
Expand Down
8 changes: 4 additions & 4 deletions test/functional/tools/sam_to_bam_native.xml → .../functional/tools/sam_to_unsorted_bam.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,13 +23,13 @@
</command>
<inputs>
<param name="input1" type="data" format="sam" label="SAM file" optional="true"/>
<param name="input2" type="data" format="bam_native" label="Unsorted BAM file" optional="true"/>
<param name="input2" type="data" format="unsorted.bam" label="Unsorted BAM file" optional="true"/>
<param name="input3" type="data" format="bam" label="BAM file sorted by coordinate" optional="true"/>
<param name="input4" type="data" format="qname_sorted.bam" label="BAM file sorted by queryname" optional="true"/>
<param name="input5" type="data" format="qname_input_sorted.bam" label="BAM file with sort order determined by the aligner" optional="true"/>
</inputs>
<outputs>
<data name="bam_native_output" format="bam_native">
<data name="bam_native_output" format="unsorted.bam">
<filter>input1 or input2</filter>
</data>
<data name="bam_output" format="bam">
Expand All @@ -46,12 +46,12 @@
<!-- Test that bam native output won't be sorted-->
<test>
<param name="input1" value="sam_with_header.sam" ftype="sam"/>
<output name="bam_native_output" file="bam_native_from_sam.bam" ftype="bam_native"/>
<output name="bam_native_output" file="bam_native_from_sam.bam" ftype="unsorted.bam"/>
</test>
<!-- Test that sam input is properly converted to bam native -->
<test>
<param name="input2" value="sam_with_header.sam" ftype="sam"/>
<output name="bam_native_output" file="bam_native_from_sam.bam" ftype="bam_native"/>
<output name="bam_native_output" file="bam_native_from_sam.bam" ftype="unsorted.bam"/>
</test>
<!-- Test that sam input is properly converted to bam -->
<test>
Expand Down
4 changes: 2 additions & 2 deletions test/functional/tools/sample_datatypes_conf.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,15 +15,15 @@
<datatype extension="fastqcssanger" type="galaxy.datatypes.sequence:FastqCSSanger" display_in_upload="true" />
<datatype extension="fastqillumina" type="galaxy.datatypes.sequence:FastqIllumina" display_in_upload="true" />
<datatype extension="sam" type="galaxy.datatypes.tabular:Sam" display_in_upload="true">
<converter file="sam_to_bam_native.xml" target_datatype="bam_native"/>
<converter file="sam_to_unsorted_bam.xml" target_datatype="unsorted.bam"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
<converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
<converter file="sam_to_bigwig_converter.xml" target_datatype="bigwig"/>
</datatype>
<datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://galaxyproject.org/learn/datatypes/#bam" />
<datatype extension="qname_input_sorted.bam" type="galaxy.datatypes.binary:BamInputSorted" mimetype="application/octet-stream" display_in_upload="false" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted based on the aligner output." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM"/>
<datatype extension="qname_sorted.bam" type="galaxy.datatypes.binary:BamQuerynameSorted" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension and sorted by queryname." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM"/>
<datatype extension="bam_native" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<datatype extension="unsorted.bam" type="galaxy.datatypes.binary:BamNative" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="to_coordinate_sorted_bam.xml" target_datatype="bam"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
Expand Down
2 changes: 1 addition & 1 deletion test/functional/tools/samples_tool_conf.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@
<tool file="column_multi_param.xml" />
<tool file="special_params.xml" />
<tool file="section.xml" />
<tool file="sam_to_bam_native.xml" />
<tool file="sam_to_unsorted_bam.xml" />
<tool file="top_level_data.xml" />
<tool file="validation_default.xml" />
<tool file="validation_sanitizer.xml" />
Expand Down