CWL "format" tag

[Thilina Manamgoda <ma...@gmail.com>]

Hi stain,



 This is an example of how format is defined in cwl tool.

$namespaces:
dct: http://purl.org/dc/terms/
foaf: http://xmlns.com/foaf/0.1/
doap: http://usefulinc.com/ns/doap#
adms: http://www.w3.org/ns/adms#
dcat: http://www.w3.org/ns/dcat#
edam: http://edamontology.org/
inputs:
- id: input
type: File
description: |
The input file can be in BAM format
(Note: BAM _must_ be sorted by position)
or <bed/gff/vcf>
format: edam:format_2572 should i resolve edam in the namespaces and
display "http://edamontology.org/format_2572" or follow different approach ?

regards,
Thilina

Re: CWL "format" tag

[Stian Soiland-Reyes <st...@apache.org>]

Hi,

Yes, I think just showing the URL is OK - loading the ontology to then
find the label there would be cool - but could be tricky to get
consistently working as ontology authors are not always so good at
making their URIs actually content-negotiatable or even to work at
all..

(And also of course it cause network hangs..)





On 18 June 2016 at 12:19, Thilina Manamgoda <ma...@gmail.com> wrote:
> Hi stain,
>
>
>
>  This is an example of how format is defined in cwl tool.
>
> $namespaces:
> dct: http://purl.org/dc/terms/
> foaf: http://xmlns.com/foaf/0.1/
> doap: http://usefulinc.com/ns/doap#
> adms: http://www.w3.org/ns/adms#
> dcat: http://www.w3.org/ns/dcat#
> edam: http://edamontology.org/
> inputs:
> - id: input
> type: File
> description: |
> The input file can be in BAM format
> (Note: BAM _must_ be sorted by position)
> or <bed/gff/vcf>
> format: edam:format_2572 should i resolve edam in the namespaces and
> display "http://edamontology.org/format_2572" or follow different approach ?
>
> regards,
> Thilina



-- 
Stian Soiland-Reyes
Apache Taverna (incubating), Apache Commons
http://orcid.org/0000-0001-9842-9718