[galaxy-dev] Help

14 Jan 2014

      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>

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

#!/bin/bash
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>

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

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

</tool>

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.notarangelo@ba.infn.it
Skype: pasquale.notarangelo_1985
Msn: pasqualenotarangelo@hotmail.it
Gmail: notarangelo.pas@gmail.com

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~