Question: Adding custom tools problems
0
gravatar for jarod_v6
2.7 years ago by
jarod_v60
Italy
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?

 

Script.py -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">
  <description>
  

</description>
  <command interpreter="python">Script.py -c $cond -r  $readset -n $prefix  </command>
  <inputs>
    <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"/>
</inputs>
  <outputs>
    <data format="tabular"  name="prefix"/>
  </outputs>
<help>

</help>

</tool>
tools • 757 views
ADD COMMENTlink modified 2.7 years ago by Bjoern Gruening4.8k • written 2.7 years ago by jarod_v60
0
gravatar for Bjoern Gruening
2.7 years ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

Hi,

have a look at from_work_dir.

Hope this helps,

Bjoern

ADD COMMENTlink written 2.7 years ago by Bjoern Gruening4.8k
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