Question: Creating simple tool to downsample sam files, doesn't complete
0
gravatar for mdgronke
5 months ago by
mdgronke10
mdgronke10 wrote:

I've written a simple tool to downsample files with a script I am running. It appears to run successfully from the std.err output, but it gives a fail when I run it in Galaxy. I'm trying to figure out what's going on.

Here's the code:

<tool id="downsample_sam" name="Downsample Sam" version="0.1.0">
        <description>Downsamples a SAM file</description>
        <command interpreter="python">downsample_sam.py '$pvalue' '$input' </command>
        <inputs>
                <param type="data" format="sam" name="input" label="Select uploaded SAM file" />
                <param type="text" name="pvalue" label="P-value" />
        </inputs>
  <outputs>
        <data name="output1" format="sam" />
  </outputs>
  <help>
Downsamples a SAM file.
  </help>

</tool>

And the stderr output from my job:

[Tue Apr 24 14:22:04 EDT 2018] net.sf.picard.sam.DownsampleSam INPUT=/usr/local/apps/galaxy/database/files/000/dataset_23.dat OUTPUT=A1_downsampled.sam PROBABILITY=0.1 RANDOM_SEED=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false

[Tue Apr 24 14:22:04 EDT 2018] Executing as root@bn16-189.dcs.mcnc.org on Linux 3.10.0-693.11.6.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_161-b14; Picard version: 1.100(1571)

INFO 2018-04-24 14:22:04 DownsampleSam Finished! Kept 84 out of 826 reads.

[Tue Apr 24 14:22:04 EDT 2018] net.sf.picard.sam.DownsampleSam done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=62390272

tools mytools sam xml galaxy • 225 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson25k • written 5 months ago by mdgronke10
1
gravatar for Hotz, Hans-Rudolf
5 months ago by
Switzerland
Hotz, Hans-Rudolf1.8k wrote:

Hi

"$output1" is missing in the command tag

if your tool writes to stdout, then you should have something like:

downsample_sam.py '$pvalue' '$input' > $output1

if your tool expects a particular option (like: -outfile), then you should have something like:

downsample_sam.py '$pvalue' '$input' -outfile $output1

etc....

Hope this helps Hans-Rudolf

ADD COMMENTlink written 5 months ago by Hotz, Hans-Rudolf1.8k
0
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There are a few choices:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson25k
1

I'll check out the downsampling tool, thanks. We're migrating from Mobyle so at the moment I'm trying to figure out which tools already exist in the toolshed.

As far as planemo, I have ran a lint on it and it said it validated the xml tags, so I didn't know where the problem lay.

ADD REPLYlink written 5 months ago by mdgronke10
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