On Tue, Jan 14, 2014 at 2:17 PM, Pasquale Notarangelo
<pasquale.notarang...@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).

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