Question: Adding custom tools problems
gravatar for jarod_v6
3.6 years ago by
jarod_v60 wrote:

Dear All,

I try to use one pipeline I develop in Galaxy. I have difficult to understand how  capture the output.

This script works and produce one file with all commands to run on server. Then I need to run.

So the problem is I need to collect all the outputs. What can I do? This is script produce some folders  and inside I have some  bam and  vcf files. How can I see? -c $cond -r  $readset -n $prefix

Why They don't take the output? How can I  see all the file inside at directory of the output?


cat Tandem.xml
<tool id="tandem" name="Trythis">

  <command interpreter="python"> -c $cond -r  $readset -n $prefix  </command>
    <param format="txt" name="cond" type="data" label="Source file"/>
<param format="txt" name="readset" type="data" label="Source file"/>

 <param name="input" type="data" format="tabular" label="Dataset"/>
    <data format="tabular"  name="prefix"/>


tools • 994 views
ADD COMMENTlink modified 3.6 years ago by Bjoern Gruening5.1k • written 3.6 years ago by jarod_v60
gravatar for Bjoern Gruening
3.6 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:


have a look at from_work_dir.

Hope this helps,


ADD COMMENTlink written 3.6 years ago by Bjoern Gruening5.1k
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