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>

<param name="inputArguments" type="text" label="ARGUMENTS" optional="false"/>

    <data format="string" name="output" />


This is the bash script of the first tool (concatenateArgumentsAndPutFile.sh):

echo "ARGUMENTS:" $@
export PathFile=/tmp/$RANDOM$RANDOM
echo $@ > $PathFile
echo "PathFile:" $PathFile

The xml of the second tool is the following:

<tool id="infnTools_InsertBiomasTools" name="InsertJobs and check the status of Biomas">
  <description>InsertJobs Biomas Tool and check the status</description>

<command interpreter="bash">insertAndCheckBiomasJobs.sh $input </command>

<param format="string" name="input" type="data" label="Insert path file"/>

    <data format="tabular" name="output"/>


When we run the workflow the output of the first tool isn't seen as input of the second tool.

Into the galaxy history we see this value for the input of the second tool: /home/pasquale/galaxy-dist/database/files/000/dataset_83.dat

Also this file is emtpy.

How we can resolve the problem?

Thanks and best regard
Pasquale & Alfonso


Dott. Pasquale Notarangelo
INFN Istituto Nazionale di Fisica Nucleare - Sezione Bari

Via Orabona, 4 - 70126 Bari, Italy

Tel. ufficio: +39 080-5443194
Interno ufficio: 3194
Mail: pasquale.notarang...@ba.infn.it
Skype: pasquale.notarangelo_1985
Msn: pasqualenotarang...@hotmail.it
Gmail: notarangelo....@gmail.com

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