Nicola, thanks a bunch! Your eyes are phenomenal!
Greg
> On Nov 4, 2015, at 8:09 PM, Nicola Soranzo <nsora...@tiscali.it> wrote:
>
> Hi Greg,
> in the inputs the param has name "input_gff", while in the test you are using
> name "input".
>
> Cheers,
> Nicola
>
> ---- Von Kuster, Greg ha scritto ----
>
>> Hello Galaxy devs,
>>
>> I’m developing a tool that uses a multi-select list to accept any number of
>> input datasets. The tool works fine when executing it within Galaxy, but
>> when running it through planemo testing, it never passes, so I’m wondering
>> if there are known issues with planemo testing tools that produce dataset
>> collections.
>>
>> I’ve spent some time adding debugging log statements into the Galaxy
>> framework for planemo test runs, but haven’t uncovered anything obvious. So
>> if there are no known issues with planemo testing dataset_collections, I’m
>> wondering if my tool config syntax is incorrect.
>>
>> Does anyone see anything obvious? Any insight is much appreciated!
>>
>> Here is the command line. Notice that I do not define any outputs since I
>> am using a dataset collection. Is this causing a problem for planemo?
>>
>> <command>
>> python $__tool_directory__/genetrack.py
>> --input_format $input_format_cond.input_format
>> #if str($input_format_cond.input_format) == "genetracktool":
>> #for $i in $input_format_cond.input_genetracktool:
>> --input "${i}" "${i.hid}" "${i.name}"
>> #end for
>> #elif str($input_format_cond.input_format) == "gff":
>> #for $i in $input_format_cond.input_gff:
>> --input "${i}" "${i.hid}" "${i.name}"
>> #end for
>> #end if
>> --sigma $sigma
>> --exclusion $exclusion
>> --up_width $up_width
>> --down_width $down_width
>> --filter $filter
>> --chromosome $chromosome
>> --chunk_size $chunk_size
>> --output_format $output_format
>> </command>
>>
>> The input dataset parameter looks like this:
>>
>> <param name="input_gff" type="data" format="gff" multiple="True"
>> label="Predict peaks on" />
>>
>> The tool produces a list of outputs, so I’ve defined a collection like this:
>>
>> <outputs>
>> <collection name="genetrack_output" type="list" label="Genetrack
>> results on ${on_string}">
>> <discover_datasets pattern="(?P<designation>.*)"
>> directory="output" ext="gff" visible="false" />
>> </collection>
>> </outputs>
>>
>> I’m using planemo, version 0.19.0.
>>
>> Here is one of the tools’ functional test definitions.
>>
>> <test>
>> <param name="input" value="genetrack_input_unsorted4.gff"
>> ftype="gff" />
>> <param name="input_format" value="gff" />
>> <param name="sigma" value="5" />
>> <param name="exclusion" value="20" />
>> <param name="up_width" value="10" />
>> <param name="down_width" value="10" />
>> <param name="filter" value="3" />
>> <param name="chromosome" value="all" />
>> <param name="chunk_size" value="10" />
>> <param name="output_format" value="gff" />
>> <output_collection name="genetrack_output" type="list">
>> <element name="s5e20u10d10F3" file="genetrack_output4.gff"
>> ftype="gff" />
>> </output_collection>
>> </test>
>>
>> Here is the log from running the test with planemo.
>>
>> Genetrack ( genetrack ) > Test-3 ...
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,292
>> Starting new HTTP connection (1): localhost
>> galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,295 Session
>> authenticated using Galaxy master api key
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,303 "GET
>> /api/users?key=test_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,305
>> Starting new HTTP connection (1): localhost
>> galaxy.web.framework.webapp INFO 2015-11-04 15:22:03,308 Session
>> authenticated using Galaxy master api key
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,326 "POST
>> /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,328
>> Starting new HTTP connection (1): localhost
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,418 "POST
>> /api/histories HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool INFO 2015-11-04 15:22:03,421
>> Starting new HTTP connection (1): localhost
>> requests.packages.urllib3.connectionpool DEBUG 2015-11-04 15:22:03,475 "POST
>> /api/tools HTTP/1.1" 400 None
>> ERROR
>>
>> ======================================================================
>> ERROR: Genetrack ( genetrack ) > Test-1
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>> File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py",
>> line 289, in test_tool
>> self.do_it( td )
>> File "/Users/gvk/work/git_workspace/galaxy/test/functional/test_toolbox.py",
>> line 58, in do_it
>> raise e
>> RunToolException: Error creating a job for these tool inputs - Unknown error
>> occurred while processing request.
>> -------------------- >> begin captured logging << --------------------
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection
>> (1): localhost
>> galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master
>> api key
>> requests.packages.urllib3.connectionpool: DEBUG: "GET
>> /api/users?key=test_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection
>> (1): localhost
>> galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master
>> api key
>> requests.packages.urllib3.connectionpool: DEBUG: "POST /api/users HTTP/1.1"
>> 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection
>> (1): localhost
>> galaxy.web.framework.webapp: INFO: Session authenticated using Galaxy master
>> api key
>> requests.packages.urllib3.connectionpool: DEBUG: "POST
>> /api/users/2891970512fa2d5a/api_key HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection
>> (1): localhost
>> requests.packages.urllib3.connectionpool: DEBUG: "POST /api/histories
>> HTTP/1.1" 200 None
>> requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection
>> (1): localhost
>> requests.packages.urllib3.connectionpool: DEBUG: "POST /api/tools HTTP/1.1"
>> 400 None
>> --------------------- >> end captured logging << ——————————
>>
>>
>> Thanks very much,
>>
>> Greg Von Kuster
>>
>>
>> ___________________________________________________________
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