Question: Tests on a tool with an input of type data_collection
0
gravatar for yliu41
11 weeks ago by
yliu4150
yliu4150 wrote:

Hello folks,

My Tool#1 is using a data_collection type created by Tool#2 as an input parameter.

<param name="trix_index" 
                type="data_collection"
                collection_type="list" 
                label="Specify Trix index" 
                help="Dataset collection containing ix and ixx files generated by UCSC Trix Index Generator"
    />

Below is how the collection is created in Tool#2:

<outputs>
    <collection name="trix_index" type="list" label="Trix index">
        <data name="index_ix" format="txt" from_work_dir="output.ix"/>
        <data name="index_ixx" format="txt" from_work_dir="output.ixx" />
    </collection>
</outputs>

Now, I want to write a test case for my Tool#1. But I am not sure how to specify individual elements "index_ix" and "index_ixx" for data_collection "trix_index" of type "list". I found an example for type "paired" (collection_paired_test.xml and tried the code as below:

<param name="trix_index">
     <collection type="list">
         <element name="index_ix" value="trix_index_files/blast_out.ix" />
         <element name="index_ixx" value="trix_index_files/blast_out.ixx" />
     </collection>
 </param>

Unfortunately, this didn't work. I got the error:

File "/home/gonramp/.dev/local/lib/python2.7/site-packages/planemo/test/results.py", line 101, in failed_ids
    if test_data["data"]["status"] == "success":
TypeError: 'NoneType' object has no attribute '__getitem__'

Thank you in advance for any hints or suggestions!

ADD COMMENTlink modified 11 weeks ago by Jennifer Hillman Jackson23k • written 11 weeks ago by yliu4150
0
gravatar for Jennifer Hillman Jackson
11 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Try using Planemo for tool development: https://galaxyproject.org/tools/

These are the areas in the docs that cover data_collections.

Hope that helps! Jen, Galaxy team

ADD COMMENTlink written 11 weeks ago by Jennifer Hillman Jackson23k
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