Hi John,
Thank you very much for your reply.
# I just want to clarify - do you have a tool with a multiple input data
# parameter (e.g. <param type="data" multiple="true" ... ) as some
# intermediate step in a workflow? Or are you using a repeat or
# something?
I have a tool with a multiple input data parameter at the end of the workflow. So, it receives the output of others. The types of output and input are the same. Here is the code of the tool:
<inputs>
<param name="input_pdbs" type="data" multiple="true" format="pdb" label="PDB Files" />
<param name="Fitness_Energy" type="select" display="checkboxes" multiple="true" label="Objective">
<option value="Potential">Potential</option>
<option value="Gyrate">Gyrate</option>
<option value="Hydrophobic">Hydrophobic</option>
<option value="Hydrophilic">Hydrophilic</option>
<option value="Area_Total">Total Area</option>
<option value="H_Bond_Main">H Bond Main</option>
<option value="Electrostatic">Stride Helix</option>
<option value="GBSA_Solvatation">GBSA_Solvatation</option>
<option value="Van_der_Waals">Van der Waals</option>
</param>
</inputs>
<outputs>
<data name="output" format="zip" label="Analysis.zip"/>
</outputs>
# And are you saying the workflow editor shows multiple inputs going
# into the tool but at runtime the tool is only actually receiving one
# of these?
No, the workflow editor doesn't show me multiple input. I was saying that I connect more than one tool to the input of this tool above. I think if I do this, Galaxy would set multiple input with the several outputs I connected, and it does. I was confused because when I ran the workflow, on the tool that should receive two output was showing just one. It would be better if Galaxy listed all the input.
I checked my instance I wasn't with the latest stable release. I updated and now it is working.
Thanks for your help John.