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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