On Tue, Jan 14, 2014 at 2:17 PM, Pasquale Notarangelo <Pasquale.Notarangelo@ba.infn.it> wrote:
Hi all, we are two new galaxy users.
We have developed 2 new tools and we would connect them into a new workflow.
We are able to import both tools and to link them into a workflow but we aren't able to pass the output of the first tool as the input of the second tool.
The first tool calls a bash script that produces a simple string (this is the path of the file generated by the script).
This is the xnl file of the first tool:
<tool id="infnTools_ConcatenateArgumentsTool" name="Concatenate Arguments and generate file Tool">
<description>Concatenate arguments strings and generate file</description>
<command interpreter="bash">concatenateArgumentsAndPutFile.sh $inputArguments</command>
<inputs> <param name="inputArguments" type="text" label="ARGUMENTS" optional="false"/> </inputs>
<outputs> <data format="string" name="output" /> </outputs>
</tool>
You've defined an input parameter and used it in the <command> definition, $inputArguments, but you never used the output filename $output in the <command> tag. That is how you tell you tool where to put the output data for Galaxy to find. (As a separate issue, I am confused about you defining format="string", if you just mean a plain text file use the existing file format definition). Peter