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Question: Galaxy Wrapper in BioLinux XML
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gravatar for rlee03
3.6 years ago by
rlee03 • 50
United States
rlee03 • 50 wrote:

Hi,

I am trying to write a wrapper to run blast on our servers, running it off the NCBI would be too slow.

I am beginning this process by looking at the galaxy tutorial

https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial

 

1) I got this GC content example to work. But was curious, in #3 Create Tool Definition of the url above,

<command interpreter="perl">toolExample.pl $input $output</command>,

what does $input mean? where is it coming from?  It cannot come from

<inputs> directly below this code, since there is a diff between inputs and input.

I have galaxy with biolinux, so an explicit file would be wonderful.

P.S. I read pretty much all of the doc on galaxy. Coping and pasting a URL will not help. Please give me a clear example since I have a limited Comp sci background. Thanks!
galaxy xml python wrapper • 950 views
ADD COMMENT • link •
modified 3.6 years ago by Martin Čech ♦♦ 4.9k • written 3.6 years ago by rlee03 • 50
0
gravatar for Martin Čech
3.6 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

The $input comes from the tool form, specificaly from

​<param format="fasta" name="input" type="data" label="Source file"/>

See the second example at https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccommand.3E_tag_set
ADD COMMENT • link modified 3.6 years ago • written 3.6 years ago by Martin Čech ♦♦ 4.9k

Hi Martin, Thank you for quick response. Specifically, Where is the $input linked to in relation to the .pl file? How does pl script know how to ineract with Mytools. XML?What can't the author make $input the second parameter while making $output the first parameter in Mytools.xml? Thanks

ADD REPLY • link written 3.6 years ago by rlee03 • 50

The Perl script is getting the arguments in its very beginning:

# usage : perl toolExample.pl <FASTA file> <output file>

open (IN, "<$ARGV[0]"); # $input
open (OUT, ">$ARGV[1]"); # $output

 

The Perl script does not need to know about the XML specifically, the script is called by Galaxy which knows what $input and $output is because the user specified it in the form.

I do not understand your third question.

ADD REPLY • link modified 3.6 years ago • written 3.6 years ago by Martin Čech ♦♦ 4.9k
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