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Question: how to get multiple bam files generated by bam split in Galaxy local
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gravatar for neerajrana14
4.2 years ago by
neerajrana14 • 40
Germany
neerajrana14 • 40 wrote:

Hi,

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>
  <inputs>
    <param format="bam" name="inputfile" type="file" label="Source file .bam generated by RGAssign"/>
  </inputs> 

Thanks.
galaxy bam • 1.7k views
ADD COMMENT • link •
modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by neerajrana14 • 40
0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

This tool in Galaxy has a very similar output to the one you describe. Perhaps it will be a useful model to work from? 
http://toolshed.g2.bx.psu.edu/view/devteam/fastx_barcode_splitter

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 COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k

Hi,

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

ADD REPLY • link written 4.2 years ago by neerajrana14 • 40
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