Question: Can I generate random output file in galaxy using XML command Tag
gravatar for Shirish
4.5 years ago by
Shirish20 wrote:


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 ./ -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/ -b $bam_file -f $fasta_file  -o /home/Data/galaxy-dist/database/files/000/ | rand .vcf  </command>

so please tell me solution on this.



tool galaxy samtools • 1.5k views
ADD COMMENTlink modified 4.5 years ago by Martin Čech ♦♦ 4.9k • written 4.5 years ago by Shirish20
gravatar for Dannon Baker
4.5 years ago by
Dannon Baker3.7k
United States
Dannon Baker3.7k 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 -- (


See an example here, specifically the "out_file1" bit.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by Dannon Baker3.7k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 183 users visited in the last hour