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>
Just a guess, but in the second case, are you sure the result data is written to the current working directory?
It should be. It is the exact same method as stated above. The only difference is the way of input (Path vs Browse)
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.
This did not fix the problem unfortunately.... :(