Question: Adding custom tools problems
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jarod_v6 • 0 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>
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modified 3.6 years ago
by
Bjoern Gruening ♦ 5.1k
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written
3.6 years ago by
jarod_v6 • 0
