Hi,
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 step?
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: http://main.g2.bx.psu.edu/u/cjav/w/fastq-joiner---input-datasets
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' Response -------- {'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' Response -------- {'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.
Thanks, Carlos