format="tabular" in galaxy tool is picking up fasta

<tool id="jb_blast2gff" name="Blast2Gff" version="1.0.0"> <description>Convert BLAST to GFF</description> <command interpreter="perl">Blast2Gff.pl -i $input1 -o $output -s $input2</command> <inputs> <param format="tabular" name="input1" type="data" label="BLAST Result file (tabular)"/> <param format="fasta" name="input2" type="data" label="Original Sequence file (FASTA)"/> </inputs> <outputs> <data format="gff" name="output" label="BLAST to GFF output file"/> </outputs> </tool>

2.5 years ago by

Hotz, Hans-Rudolf • 1.8k

Switzerland

Hotz, Hans-Rudolf • 1.8k wrote:

just double checking:

are you sure, you are editing the right tool xml file? i.e. the one which is linked in the 'tool_conf.xml' file?
do you reload the tool xml file (via the admin page) after each change?
does the tabular file show up in the drop down at all?
have you changed anything the hierarchy of data formats?

Regards, Hans-Rudolf

ADD COMMENT • link written 2.5 years ago by Hotz, Hans-Rudolf • 1.8k

Thanks for the reply.

are you sure, you are editing the right tool xml file? i.e. the one which is linked in the 'tool_conf.xml' file?

yes, I sanity checked the configs by changing some text in the xml files. They are the right files.

do you reload the tool xml file (via the admin page) after each change?

I restart the galaxy server and refresh the browser, if that's what you mean. yes, each time I change.

does the tabular file show up in the drop down at all?

yes, both tabular and fast show up in this tool. In the other tool where I specify gff format, gff files DO NOT show up.

have you changed anything the hierarchy of data formats?

no, I only added tool_conf.xml and my tools.

Other Note: I have NCBI Blast tools installed and blast databases. These were installed by toolshed and they are working fine.

ADD REPLY • link modified 2.5 years ago • written 2.5 years ago by eric • 0

ok, this is strange.....I can't promise, but I will try to reproduce on our dev server later today

ADD REPLY • link written 2.5 years ago by Hotz, Hans-Rudolf • 1.8k

I took your xml file (as you have posted it in your original mail) and I can reproduce your problem. At the moment, this doesn't make sense at all to me. "fasta" should not be a sub-format of tabular in my opinion. I will try and dig deeper. -or maybe someone from the core-team can enlighten us.

Regards, Hans-Rudolf

ADD REPLY • link written 2.5 years ago by Hotz, Hans-Rudolf • 1.8k

Ah, thanks for saving my sanity. I'll post it as an issue.

ADD REPLY • link written 2.5 years ago by eric • 0

Hi -

Fasta is included in tabular, it saves time with certain manipulation tools and I think it is a good thing to keep. Other data that is tab delimited, but with a non-tabular datatype assignment, will also appear. "Tabular" is fairly generic and global this way on purpose. The reverse one would not want (any tabular data showing up when fasta/vcf/etc specified).

It was the gff mentioned that seems to be the core problem. What happens if the target input dataset is assigned the datatype "gff3"? Does it appear in the menu?

Some tools state "gff" is the input type when the actual type needed is "gff3". Gff/gtf are similar to each other, but very different from gff3. I am not sure of the why behind this logic of substituting gff for gff3 .. except maybe to simply the UI? Specific seems better, imho. Nor do I know the details of the datatype filtering for gff (how specific/expanded the datatype class is). It is in github though.

Maybe helps? Jen, Galaxy team

ADD REPLY • link modified 2.5 years ago • written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks Jen, The gff3 trick (changing the output format="gff3" of the prior stage) works!

I guess the remaining question is, how do I get it to specifically choose only a tabular file rather than fasta?

ADD REPLY • link modified 2.5 years ago • written 2.5 years ago by eric • 0

Thank you very much Jen! There is always something new I learn about the inner workings of Galaxy...or rather I have to relearn, because I have already forgotten it over time ;)

ADD REPLY • link written 2.5 years ago by Hotz, Hans-Rudolf • 1.8k

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