mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
John Chilton
ec24396140
Long term this could allow Galaxy to support - multiple tooling formats (Galaxy-like YAML, CWL http://bit.ly/cwltooldesc, etc...). But I think it is also important from a purely design perspective - this is a core logic class integrating different components - they should not also be doing XML parsing. To verify the interface for parsing tools is expressive enough to allow multiple useful implementations, I built a test YAML tool description that implements many of the same features as Galaxy but smooths out rough edges (uses exit codes for job failure by default for instance). Loading these tools is disabled by default and it is not documented how to enable them because they are not intended to be part of Galaxy's public API.
82 lines
1.6 KiB
YAML
82 lines
1.6 KiB
YAML
id: simple_constructs_y
|
|
name: simple_constructs_y
|
|
version: 1.0
|
|
command:
|
|
>
|
|
echo "$booltest" >> $out_file1;
|
|
echo "$inttest" >> $out_file1;
|
|
echo "$floattest" >> $out_file1;
|
|
cat "$simp_file" >> $out_file1;
|
|
cat "$more_files[0].nestinput" >> $out_file1;
|
|
echo "$p1.p1val" >> $out_file1;
|
|
inputs:
|
|
- name: booltest
|
|
type: boolean
|
|
truevalue: booltrue
|
|
falsevalue: boolfalse
|
|
checked: false
|
|
- name: inttest
|
|
type: integer
|
|
value: 1
|
|
- name: floattest
|
|
type: float
|
|
value: 1.0
|
|
- name: simp_file
|
|
type: data
|
|
- name: more_files
|
|
label: "More Files"
|
|
type: repeat
|
|
blocks:
|
|
- type: data
|
|
name: nestinput
|
|
- name: p1
|
|
type: conditional
|
|
test:
|
|
type: boolean
|
|
name: p1use
|
|
when:
|
|
true:
|
|
- name: p1val
|
|
type: text
|
|
value: p1used
|
|
false:
|
|
- name: p1val
|
|
type: text
|
|
value: p1notused
|
|
|
|
outputs:
|
|
out_file1:
|
|
format: txt
|
|
tests:
|
|
- inputs:
|
|
booltest: true
|
|
inttest: 12456
|
|
floattest: 6.789
|
|
simp_file: simple_line.txt
|
|
nestinput: simple_line_alternative.txt
|
|
p1use: true
|
|
outputs:
|
|
out_file1:
|
|
asserts:
|
|
has_line:
|
|
line: booltrue
|
|
has_line:
|
|
line: 12456
|
|
has_line:
|
|
line: 6.789
|
|
has_line:
|
|
line: "This is a line of text."
|
|
has_line:
|
|
line: "This is a different line of text."
|
|
has_line:
|
|
line: p1used
|
|
- inputs:
|
|
simp_file: simple_line.txt
|
|
nestinput: simple_line_alternative.txt
|
|
p1use: false
|
|
outputs:
|
|
out_file1:
|
|
asserts:
|
|
has_line:
|
|
line: p1notused
|