Question: how to get multiple bam files generated by bam split in Galaxy local
gravatar for neerajrana14
4.2 years ago by
neerajrana1440 wrote:


I want to add a small tools using bam to my local Galxy server.if i run this command on linux command line it generate one bam file into 96 bam file in the directory directly .

 bamtools split -in inputfile.bam -stub split -tag RG

I want to make an HTML page as output from Galaxy from where i can download all 96 files one buy one or at once by select all.

I am new to galaxy and i just wrote few lines in XML code .How can i proceed it further.

<tool id="bamtesting" name="bamtest">

  <description>bam tools to split RGAssign file into smaple file</description>
  <command> bamtools split -in $inputfile -stub split -tag RG </command>
    <param format="bam" name="inputfile" type="file" label="Source file .bam generated by RGAssign"/>


galaxy bam • 1.7k views
ADD COMMENTlink modified 4.2 years ago by Jennifer Hillman Jackson25k • written 4.2 years ago by neerajrana1440
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This tool in Galaxy has a very similar output to the one you describe. Perhaps it will be a useful model to work from?

I should let you know that some users find it annoying that the output files are not datasets in a history (the files can be downloaded or the file URLs can be used with the "Get Data -> Load File" tool to add then to a history). There is an alternate repository in the Tool Shed for this tool that changes the output style - you may want to examine that one as well. I just wanted to let you know about this as you proceed with design.

Best, Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k


Thanks for you reply.I am woking on it and let you know if it works with my tool.

ADD REPLYlink written 4.2 years ago by neerajrana1440
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