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Merge pull request #6385 from dannon/revert-baiconverter-removal

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[18.01] Revert "Remove bam to bai converter"
This commit is contained in:
Martin Cech
2018-06-22 13:08:13 -05:00
committed by GitHub
parent 48fafa8096 5f24794efd
commit 36706e9eb3
2 changed files with 16 additions and 0 deletions
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config/datatypes_conf.xml.sample
+2
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@@ -9,6 +9,7 @@
<datatype extension="axt" type="galaxy.datatypes.sequence:Axt" display_in_upload="true" description="blastz pairwise alignment format. Each alignment block in an axt file contains three lines: a summary line and 2 sequence lines. Blocks are separated from one another by blank lines. The summary line contains chromosomal position and size information about the alignment. It consists of 9 required fields." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Axt"/>
<datatype extension="fli" type="galaxy.datatypes.tabular:FeatureLocationIndex" display_in_upload="false"/>
<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://wiki.galaxyproject.org/Learn/Datatypes#BAM">
<converter file="bam_to_bai.xml" target_datatype="bai"/>
<converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
<converter file="to_qname_sorted_bam.xml" target_datatype="qname_sorted.bam"/>
<display file="ucsc/bam.xml" />
@@ -17,6 +18,7 @@
<display file="igb/bam.xml" />
<display file="iobio/bam.xml" />
</datatype>
<datatype extension="bai" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="false"/>
<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>
<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">
lib/galaxy/datatypes/converters/bam_to_bai.xml
+14
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@@ -0,0 +1,14 @@
<tool id="CONVERTER_Bam_Bai_0" name="Bam to Bai" version="1.0.0" hidden="true">
<requirements>
<requirement type="package">samtools</requirement>
</requirements>
<command>samtools index '$input1' '$output1'</command>
<inputs>
<param format="bam" name="input1" type="data" label="Choose BAM"/>
</inputs>
<outputs>
<data format="bai" name="output1"/>
</outputs>
<help>
</help>
</tool>