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.notarang...@ba.infn.it
Skype: pasquale.notarangelo_1985
Msn: pasqualenotarang...@hotmail.it
Gmail: notarangelo....@gmail.com
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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