Hi all,

Using gzipped input files in tool functional tests (which would be
decompressed by the upload tool) used to work, e.g.


But with more recent versions of Galaxy this has broken, e.g.


According to the TravisCI failure, the command run was:

-i "None" -f "data" -m lax -p

In this case the -i argument was $input_file, and -f was its
extension/datatype. Somehow the gzipped FASTQ was
not found, which is why the filename is just "None" and
its datatype the default "data".

My tool is sensibly returning error code 1, and:

Missing input file: 'None'

I have made some minor changes to this tool between those
TravisCI tests, but the test is the same:

        <param name="input_file" value="SRR639755_mito_pairs.fastq.gz"
ftype="fastqsanger" />
        <param name="mapping_file"
value="SRR639755_sample_by_coord.sam" ftype="sam" />
        <param name="pair_mode" value="lax" />
        <param name="output_choice" value="pos" />
        <output name="output_pos" file="SRR639755_sample_lax.fastq"
ftype="fastqsanger" />
        <param name="input_file" value="SRR639755_mito_pairs.fastq.gz"
ftype="fastqsanger" />
        <param name="mapping_file"
value="SRR639755_sample_by_coord.sam" ftype="sam" />
        <param name="pair_mode" value="strict" />
        <param name="output_choice" value="pos" />
        <output name="output_pos" file="SRR639755_sample_strict.fastq"
ftype="fastqsanger" />


I could reproduce this on my development machine running an
older Galaxy:

$ hg log | head
changeset:   16732:212e1d5e9be5
branch:      stable
tag:         tip
parent:      16716:2db0fb9594d6
parent:      16731:7adac1842adf
user:        John Chilton <jmchil...@gmail.com>
date:        Wed Dec 10 12:20:55 2014 -0500
summary:     Merged in dannon/galaxy-central/stable (pull request #602)

And again updating to the current tip,

$ hg log | head
changeset:   16850:e614c7c1e0e9
tag:         tip
parent:      16848:1cf0af0a6324
parent:      16849:d13f2b265dbf
user:        Dannon Baker <dannon.ba...@gmail.com>
date:        Tue Dec 16 15:48:44 2014 -0500
summary:     Merged in nitesh1989/galaxy-central3 (pull request #615)

I can "fix" it by swapping the gzipped test input_file
SRR639755_mito_pairs.fastq.gz to the uncompressed
SRR639755_mito_pairs.fastq instead, as in this commit:


I would like to revert this workaround since the uncompressed
FASTQ file is a bit large to bundle as a test case - so I hope
this is simply due to an accidental regression in Galaxy itself.


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