Unverified Commit 0611465e authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Fix output datatype when uncompressing a dataset with incorrect datatype 

with the ``CONVERTER_gz_to_uncompressed`` tool.

Previously, if a user forced an incorrect datatype to a compressed input
dataset (e.g. `fastqsanger` instead of `fastqsanger.gz`), then the output
datatype assigned by this tool would be an invalid one (`fastqsan`).

Fix #17938.
parent 77fc8494

lib/galaxy/datatypes/converters/gz_to_uncompressed.xml

+10 −1
Original line number Diff line number Diff line
@@ -6,7 +6,7 @@ gzip -dcf '$input1' > '$output1' 
    <configfiles>

        <configfile name="ext_config">{"output1": {

  "name": "${input1.name[0:-len('.gz')] if $input1.name.endswith('.gz') else $input1.name} uncompressed",

  "ext": "${input1.ext[0:-len('.gz')] if $input1.ext != 'vcf_bgzip' else 'vcf'}"

  "ext": "${'vcf' if $input1.ext == 'vcf_bgzip' else $input1.ext[0:-len('.gz')] if $input1.ext.endswith('.gz') else $input1.ext}"

}}</configfile>

    </configfiles>

    <inputs>
@@ -21,6 +21,15 @@ gzip -dcf '$input1' > '$output1' 
            <param name="input1" value="test.vcf.gz" ftype="vcf_bgzip"/>

            <output name="output1" file="test.vcf" ftype="vcf"/>

        </test>

        <test>

            <param name="input1" value="1.fasta.gz" ftype="fasta.gz"/>

            <output name="output1" file="1.fasta" ftype="fasta"/>

        </test>

        <!-- Test input with wrong format -->

        <test>

            <param name="input1" value="1.fasta.gz" ftype="fasta"/>

            <output name="output1" file="1.fasta" ftype="fasta"/>

        </test>

    </tests>

    <help>

    </help>