Python outputs empty on history

Question: Python outputs empty on history

3 months ago by

Hello!

So I have a python script that I'm integrated in my local galaxy and it outputs 2 files: one pdf created with pdflatex and one csv file. This code works perfectly on the command line, on galaxy the code finishes successfully but the outputs are empty.

Command on the xml:

<command detect_errors="exit_code"><![CDATA[
    python '$__tool_directory__/LungCARD_report.py' "$patientID" "$sampleID" "$birthday" "$gender" "$labKit" "$sequencer" "$vcf_file" "$idxstats" "$flagstat" "$fastq1" "$fastq2"
]]></command>

Writting of the pdf file:

with open(filename, 'w') as f:
    f.write(content)

#outputs the report as latex
commandLine = subprocess.Popen(['pdflatex', filename])
commandLine.communicate()

os.unlink(filename)
os.unlink(filename[:-4] + '.log')
os.unlink(filename[:-4] + '.aux')

Writting of the csv file:

vcf.getVCF().to_csv(filename)

Planemo wrote the outputs tag as:

<outputs>
<data name="output1" format="pdf" from_work_dir="report.pdf" />
<data name="output2" format="csv" from_work_dir="unknown_variants.csv" />
</outputs>

Please help me get the outputs to the history in galaxy! Thanks!

outputs tool development galaxy custom • 228 views

ADD COMMENT • link •

written 3 months ago by luciaaheitor • 20

I never used "from_work_dir" so not sure about that. Maybe it needs to be the full path.

I would use $output1 as parameter for the python script. So:

python '$__tool_directory__/LungCARD_report.py' "$patientID" "$sampleID" "$birthday" "$gender" "$labKit" "$sequencer" "$vcf_file" "$idxstats" "$flagstat" "$fastq1" "$fastq2" $output1 $output2

In the python script I write the result to the $output1 parameter

ADD REPLY • link written 3 months ago by gb • 60

I changed the xml as you suggested and the result is the same.

In the python script I write the result to the $output1 parameter

How do you do that? I think the problem might be from my script but even after researching about it I was still unaware of what to do..

ADD REPLY • link modified 3 months ago • written 3 months ago by luciaaheitor • 20

3 months ago by

gb • 60

gb • 60 wrote:

So you pass the variable $output1 from the xml file into your python script. The variable $output1 is basically just a path, a output location.

So for example this:

with open(filename, 'w') as f:
f.write(content)

The filename should be the $output1 value.

ADD COMMENT • link written 3 months ago by gb • 60

Thank you! Thanks to your explanation I figured out what I was doing wrong.

The problem was that galaxy was looking for the "report.pdf" and "unknown_variants.csv" and the script was giving them other file names. After changing this everything worked out fine!

Thank you once again for the patience :)

ADD REPLY • link written 3 months ago by luciaaheitor • 20

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