Question: from_work_dir tags not working in Galaxy output
0
gravatar for KeyGene
3.7 years ago by
KeyGene10
Netherlands
KeyGene10 wrote:

Hi,

 

I've got a problem and I hope you know what I am doing wrong. I'm running/coding a tool thats able to take inputs on two different ways: via a upload system and then select it from your history, or via an absolute data path. If I run the tool bij uploading the files, it works fine. If I run the tool by applying the data paths to the two files, the output remains empty. In both cases output should be written to output.1.fastq and output.2.fastq. Anyone knows why this won't work for applying data paths? The differences between browsing and applying data paths is only this; type="text" vs type="data". (And yes, the data paths do exist since the tool is running for at least a few minutes)

Works:

   <outputs>
    <data format="fastq" name="output.1.fastq" from_work_dir="output.1.fastq">
      <filter>(selectSet.browsePaired[selectPairedBrowse] == "doPairedBrowse")</filter>
    </data>
    <data format="fastq" name="output.2.fastq" from_work_dir="output.2.fastq">
      <filter>(selectSet.browsePaired[selectPairedBrowse] == "doPairedBrowse")</filter>
    </data>
  </outputs> 

Does not work:

   <outputs>
    <data format="fastq" name="output.1.fastq" from_work_dir="output.1.fastq">
      <filter>(selectSet.pathPaired[selectPairedPath] == "doPairedPath")</filter>
    </data>
    <data format="fastq" name="output.2.fastq" from_work_dir="output.2.fastq">
      <filter>(selectSet.pathPaired[selectPairedPath] == "doPairedPath")</filter>
    </data>
  </outputs> 

dev tags config tools output • 1.4k views
ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by KeyGene10
1

Just a guess, but in the second case, are you sure the result data is written to the current working directory?

ADD REPLYlink written 3.7 years ago by Bjoern Gruening5.1k

It should be. It is the exact same method as stated above. The only difference is the way of input (Path vs Browse)

ADD REPLYlink written 3.7 years ago by KeyGene10
1

I would very strongly encourage you not to put periods in the output names like that. Can you name the outputs `output1` and `ouptut2` but keep the from_work_dir the same? I bet that would fix the problem if the files are actually there.

ADD REPLYlink written 3.7 years ago by jmchilton1.1k

This did not fix the problem unfortunately.... :(

ADD REPLYlink written 3.7 years ago by KeyGene10
2
gravatar for KeyGene
3.7 years ago by
KeyGene10
Netherlands
KeyGene10 wrote:

Hi all! Apologies, but it turned to be an error in de script itself. Weird though there wasn't a sterr produced, but ok. 

ADD COMMENTlink written 3.7 years ago by KeyGene10

Thanks for posting the solution and for closing out the question with an accepted answer (even if is your own!). Appreciated :) Jen, Galaxy team

ADD REPLYlink written 3.7 years ago by Jennifer Hillman Jackson25k
0
gravatar for KeyGene
3.7 years ago by
KeyGene10
Netherlands
KeyGene10 wrote:

I don't know if this helps for any if you, but if I check the directory where files should be made, the output files remain empty for the analysis done with adding filepaths, and contain data for the analysis done with the browsing function.

/opt/galaxy-dev/galaxy-dist/database/files/004

-rw-rw-r--. 1 galaxy-dev galaxy-dev        0 Oct 26 21:36 dataset_4223.dat
-rw-rw-r--. 1 galaxy-dev galaxy-dev        0 Oct 26 21:36 dataset_4224.dat

 

 

ADD COMMENTlink written 3.7 years ago by KeyGene10
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