Hi,
When trying to launch a Bismark with bowtie2 I get the following error:
Error executing tool: Required dependency 'mate_list[0]' not found in incoming values
I can't see any problem in the bismark_bowtie2_wrapper.xml and the problem only occurs when selecting "paired-end" AND selecting "Full parameter list".
Any ideas what might be wrong?
Thanks,
Cristian
Thanks for the bug-report.
Are you able to test the latest release from: https://testtoolshed.g2.bx.psu.edu/view/bgruening/bismark
Hi Bjoern,
I could not install the latest release as it failed at compiling bowtie and bowtie2 (which were already compiled). It messed up the installation of version 0.10.1 rev 91f07ff056ca. So I reinstalled the stable version.
The log in web0.log is as follows:
galaxy.tools.actions DEBUG 2015-01-27 17:30:15,348 Dataset output filter failed: 'supressed_read_file'
galaxy.tools ERROR 2015-01-27 17:30:15,425 Exception caught while attempting tool execution:
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2240, in handle_single_execution
job, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line 2804, in execute
return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 270, in execute
handle_output( name, output )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/actions/__init__.py", line 264, in handle_output
output.actions.apply_action( data, output_action_params )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 28, in apply_action
action.apply_action( output_dataset, other_values )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 90, in apply_action
case.apply_action( output_dataset, other_values )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 61, in apply_action
return super( ToolOutputActionConditionalWhen, self ).apply_action( output_dataset, other_values )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 28, in apply_action
action.apply_action( output_dataset, other_values )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 261, in apply_action
value = self.option.get_value( other_values )
File "/home/galaxy/galaxy-dist/lib/galaxy/tools/parameters/output.py", line 188, in get_value
assert ref_name in value, "Required dependency '%s' not found in incoming values" % ref_name
AssertionError: Required dependency 'mate_list[0]' not found in incoming values
Hope this helps,
Cristian
HI Christian,
it's not yet on the main Tool Shed. I would like to test it before, but will release it as soon as possible to the main ToolShed.
Hi Bjoern,
I got a new look at the wrapper today and found the problem.
In the output filter there is a missing p in supressed_read_file. I added the missing p and it is working! I read that part of the code a dozen times and I did not see the missing p till now!
Cheers!
Cristian
Oh intesting! Do you mind to create a pull request? https://github.com/bgruening/galaxytools/tree/master/bismark_wrapper. Otherwise I will patch it tomorrow.
Thanks!
Hi Bjoern,
The diff below is against the toolshed version. Your github version is already corrected.
Cheers and thanks a lot for your work!
Cristian
diff -r 91f07ff056ca bismark_bowtie2_wrapper.xml
--- a/bismark_bowtie2_wrapper.xml Mon Apr 14 16:43:14 2014 -0400
+++ b/bismark_bowtie2_wrapper.xml Sun Feb 08 16:13:53 2015 +0100
@@ -286,7 +286,7 @@
<data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
<filter>singlePaired['sPaired'] == "paired"</filter>
<filter>params['settingsType'] == "custom"</filter>
- <filter>params['supressed_read_file'] is True</filter>
+ <filter>params['suppressed_read_file'] is True</filter>
<actions>
<conditional name="singlePaired.sPaired">
<when value="single">
