Merge pull request #5674 from jmchilton/unsorted_bam_rename

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

config/datatypes_conf.xml.sample

@@ -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"/>
@@ -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"/>

doc/source/releases/18.01.rst

@@ -1181,4 +1181,4 @@ Fixes
 .. _Pull Request 5663: https://github.com/galaxyproject/galaxy/pull/5663
 .. _Pull Request 5664: https://github.com/galaxyproject/galaxy/pull/5664
 .. _Pull Request 5665: https://github.com/galaxyproject/galaxy/pull/5665
-
+.. _Pull Request 5674: https://github.com/galaxyproject/galaxy/pull/5674

doc/source/releases/18.01_announce.rst

@@ -50,12 +50,12 @@ 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.
 
-  `Pull Request 5180`_, `Pull Request 5589`_, `Pull Request 5532`_, `Pull Request 5644`_
+  `Pull Request 5180`_, `Pull Request 5589`_, `Pull Request 5532`_, `Pull Request 5644`_, `Pull Request 5674`_
 
 **Experimental Job Caching**
   Galaxy can now be configured to allow users the option of skipping duplicated jobs if one with

lib/galaxy/datatypes/binary.py

@@ -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)

lib/galaxy/datatypes/converters/bam_to_bigwig_converter.xml

@@ -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"/>

lib/galaxy/datatypes/converters/sam_to_bam_native.xml → lib/galaxy/datatypes/converters/sam_to_unsorted_bam.xml

@@ -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>
@@ -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>

lib/galaxy/datatypes/converters/to_coordinate_sorted_bam.xml

@@ -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"/>

lib/galaxy/datatypes/converters/to_qname_sorted_bam.xml

@@ -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"/>

lib/galaxy/datatypes/sniff.py

@@ -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'

test/functional/tools/sam_to_bam_native.xml → test/functional/tools/sam_to_unsorted_bam.xml

@@ -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">
@@ -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>

test/functional/tools/sample_datatypes_conf.xml

@@ -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"/>

test/functional/tools/samples_tool_conf.xml

@@ -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" />