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Question: Can I generate random output file in galaxy using XML command Tag
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gravatar for Shirish
4.5 years ago by
Shirish • 20
India
Shirish • 20 wrote:

Hii 

I integrate the SoftSearch tool in galaxy project it will generate .vcf file but i want to generate new random  .vcf file after execution of SoftSearch tool.

if I execute by command prompt it will generate random file successfully. command used

$n=$RANDOM | perl ./SoftSearch.pl -b Small_test.bam -f chr1.small.fa -o $n.vcf

But when I execute it by GUI in xml file it will generate the error..

rand: unknown option -- '.vcf'
Can't write files here!

here is my xml command.

<command> samtools index $bam_file ; samtools faidx $fasta_file ;   /home/Data/2.4/src/SoftSearch.pl -b $bam_file -f $fasta_file  -o /home/Data/galaxy-dist/database/files/000/ | rand .vcf  </command>

so please tell me solution on this.

Thanks...

 
tool galaxy samtools • 1.5k views
ADD COMMENT • link •
modified 4.5 years ago by Martin Čech ♦♦ 4.9k • written 4.5 years ago by Shirish • 20
1
gravatar for Dannon Baker
4.5 years ago by
Dannon Baker ♦ 3.7k
United States
Dannon Baker ♦ 3.7k wrote:

I might be misinterpreting it, but it doesn't look like what you have in your command matches what's in the line you're using above.  What's the intent here -- just to generate a random filename?  And, why?

The issue is that the statement `rand .vcf` doesn't work ( in a shell or otherwise ) -- rand takes no arguments:

yoplait@anvil:~$ rand .vcf
rand: unknown option -- '.vcf'

 

It looks like you should probably be using a formal galaxy dataset output -- (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Coutputs.3E_tag_set).

 

See an example here, specifically the "out_file1" bit.  https://bitbucket.org/galaxy/galaxy-central/src/c0832d30e315c24dcc2cf23918e4b0bd7b30ba56/tools/filters/CreateInterval.xml?at=default
ADD COMMENT • link modified 4.5 years ago • written 4.5 years ago by Dannon Baker ♦ 3.7k
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