Looking at workflow_execute.py, it seems to me there can be only one
input for step, is this correct? or is there a wait to map more than
one input and match them to an specific position in a  particularly

This is the workaround I found.

I created 'Input Dataset' boxes for all of my inputs, then I linked
them to the step where they are needed. This is actually very
convenient if the same input is used in more than one step, as when I
run the workflow manually I only need to select each input once. I
tried doing this, as each 'Input Dataset' would have his own step.

This is an example workflow:

Initially I ran into this issue:
$ ./workflow_execute.py my_key http://main.g2.bx.psu.edu/api/workflows
fcfa9ae643d37c32 'Fastq joiner - Input Datasets'
'1=ldda=b4c5be159c8057c2' '2=ldda=ea0e32961d454539'
HTTP Error 400: Bad Request
"Workflow cannot be run because an expected input step '517620' has no
input dataset."

I then found you can do:
$ ./display.py my_key http://main.g2.bx.psu.edu/api/workflows/fcfa9ae643d37c32
Member Information
url: /api/workflows/fcfa9ae643d37c32
inputs: {'517620': {'value': '', 'label': 'Left-hand Reads'},
'517622': {'value': '', 'label': 'Right-hand Reads'}}
id: fcfa9ae643d37c32
name: Fastq joiner - Input Datasets

I see inputs get different keys and I can use them when executing the workflow:
$ ./workflow_execute.py my_key http://main.g2.bx.psu.edu/api/workflows
fcfa9ae643d37c32 'hist_id=9fbfd3a1be8b7f8e'
'517620=hda=8d89405199368bb0' '517622=hda=5c93f30078e5ac25'
{'outputs': ['f7c4b0900d8f3b1b'], 'history': '9fbfd3a1be8b7f8e'}

This worked perfectly. I still think it would be easier to be able to
use the step number, but this works.

Lastly, I did run into one issue where I had to import the datasets
firsts, as trying to use ldda like this:
$ ./workflow_execute.py my_key http://main.g2.bx.psu.edu/api/workflows
fcfa9ae643d37c32 'Fastq joiner - Input Datasets'
'517620=ldda=b4c5be159c8057c2' '517622=ldda=ea0e32961d454539'
{'outputs': ['44c033fad737acc5'], 'history': '9fbfd3a1be8b7f8e'}

I got this error in the history:
input data 1 (file:
/galaxy/main_database/files/002/780/dataset_2780871.dat) was deleted
before the job started

This didn't happen in our local instance using galaxy-central.

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