Re: [galaxy-dev] 'Boolean' parameter type misbehaves in tool tests if truevalue starts with hyphen?
I am with Peter that the best thing to do is probably to specify true or false. We just had a similar report from Bjoern though - the thinking being that this was probably allowed in the past (using the truevalue/falsevalue) but Galaxy lost that functionality - https://trello.com/c/iGk3f1pE. https://github.com/bgruening/galaxytools/commit/df4fdcb526df17094e03372a76763572f2095be7#commitcomment-11073612 -John On Fri, May 8, 2015 at 10:16 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, May 8, 2015 at 3:05 PM, Peter Briggs peter.bri...@manchester.ac.uk wrote: Hello I'm currently writing tests for a tool and think I've found a situation where the behaviour of the boolean parameter type does not seem correct within the test environment. The tool defines the following boolean parameter: param name=spmr type=boolean truevalue=--SPMR falsevalue= checked=False ... / and accesses its value in the command tag using: -B $spmr i.e. if the boolean is true then this should output -B --SPMR, if not then it should output -B . This appears to work as expected when the tool is installed and used interactively. But when running the tests the 'falsevalue' is always returned, even if the value is set to the 'truevalue' in the tests i.e.: param name=spmr value=--SPMR / and param name=spmr value= / both return -B . I think you may need to set the value to true/false here, e.g. https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_bam2fq/samtools_bam2fq.xml (It would be clearer if the test framework insisted on this, but it may be allowing the truevalue or falsevalue to be used - at least when they don't start with a minus sign?) Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] trinity tool form not allowing None input for strand-specificity
Hi all, I have encountered a problem when trying to run trinityrnaseq (Galaxy Tool Version 0.0.1) from Galaxy. Leaving the strand-specificity input parameter as None will prevent the form from being submitted. Instead, the strand-specificity input box will be highlighted in red and I'm asked to Please verify this parameter. Before the last update we were running a very very old instance of Galaxy (I think the update before the last was in 2013) from which we could submit trinity-jobs just fine. I found a commit from Aysam from late 2014 which does something in the immediate vicinity of the Please verify this parameter - message. (https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/), which I am guessing could have something to do with it. Anyone got any ideas regarding this? Any help would be appreciated. Thanks Christian -- Dr. Christian Schudoma Bioinformatics Support Officer Bioinformatics Group The Sainsbury Laboratory Norwich Research Park Norwich NR4 7UH United Kingdom ** +44 (0) 1603 450 601 christian.schud...@tsl.ac.ukmailto:christian.schud...@tsl.ac.uk twitter: @cpt_bwt ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] 'Boolean' parameter type misbehaves in tool tests if truevalue starts with hyphen?
Hello Peter C. Thanks for the prompt response - yes, using 'true' and 'false' in the tests seems to work for my simple example (as do 'True' and 'False'). However I suspect that there is something else going on in the real tool that I'm trying to test, as I still can't get this to work - so I'm going to have to keep investigating. At least now I know that I'm setting the booleans properly in the tests (and will add that to my list of gotchas). Thanks again for your help, best wishes Peter -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 From: Peter Cock [p.j.a.c...@googlemail.com] Sent: Friday, May 08, 2015 3:16 PM To: Peter Briggs Cc: galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] 'Boolean' parameter type misbehaves in tool tests if truevalue starts with hyphen? On Fri, May 8, 2015 at 3:05 PM, Peter Briggs peter.bri...@manchester.ac.uk wrote: Hello I'm currently writing tests for a tool and think I've found a situation where the behaviour of the boolean parameter type does not seem correct within the test environment. The tool defines the following boolean parameter: param name=spmr type=boolean truevalue=--SPMR falsevalue= checked=False ... / and accesses its value in the command tag using: -B $spmr i.e. if the boolean is true then this should output -B --SPMR, if not then it should output -B . This appears to work as expected when the tool is installed and used interactively. But when running the tests the 'falsevalue' is always returned, even if the value is set to the 'truevalue' in the tests i.e.: param name=spmr value=--SPMR / and param name=spmr value= / both return -B . I think you may need to set the value to true/false here, e.g. https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_bam2fq/samtools_bam2fq.xml (It would be clearer if the test framework insisted on this, but it may be allowing the truevalue or falsevalue to be used - at least when they don't start with a minus sign?) Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] 'Boolean' parameter type misbehaves in tool tests if truevalue starts with hyphen?
Hello I'm currently writing tests for a tool and think I've found a situation where the behaviour of the boolean parameter type does not seem correct within the test environment. The tool defines the following boolean parameter: param name=spmr type=boolean truevalue=--SPMR falsevalue= checked=False ... / and accesses its value in the command tag using: -B $spmr i.e. if the boolean is true then this should output -B --SPMR, if not then it should output -B . This appears to work as expected when the tool is installed and used interactively. But when running the tests the 'falsevalue' is always returned, even if the value is set to the 'truevalue' in the tests i.e.: param name=spmr value=--SPMR / and param name=spmr value= / both return -B . More generally: I've written a small tool to investigate the issue, and it appears that the errant behaviour only manifests when the 'truevalue' starts with a hyphen (e.g. using -Yes is broken, but Yes is okay). The demo tool is available via https://gist.github.com/pjbriggs/5bfbcf22f72e0266e61 and I've been using planemo v0.7.0 to run the tests (planemo t --install_galaxy boolean_test_issue.xml). Have I done something wrong here or is this a genuine bug? Thanks for your help, best wishes Peter -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] 'Boolean' parameter type misbehaves in tool tests if truevalue starts with hyphen?
On Fri, May 8, 2015 at 3:05 PM, Peter Briggs peter.bri...@manchester.ac.uk wrote: Hello I'm currently writing tests for a tool and think I've found a situation where the behaviour of the boolean parameter type does not seem correct within the test environment. The tool defines the following boolean parameter: param name=spmr type=boolean truevalue=--SPMR falsevalue= checked=False ... / and accesses its value in the command tag using: -B $spmr i.e. if the boolean is true then this should output -B --SPMR, if not then it should output -B . This appears to work as expected when the tool is installed and used interactively. But when running the tests the 'falsevalue' is always returned, even if the value is set to the 'truevalue' in the tests i.e.: param name=spmr value=--SPMR / and param name=spmr value= / both return -B . I think you may need to set the value to true/false here, e.g. https://github.com/peterjc/pico_galaxy/blob/master/tools/samtools_bam2fq/samtools_bam2fq.xml (It would be clearer if the test framework insisted on this, but it may be allowing the truevalue or falsevalue to be used - at least when they don't start with a minus sign?) Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] trinity tool form not allowing None input for strand-specificity
Hi Christian, was the trinityrnaseq tool installed from the Tool Shed? Which repository? Just to check this is not a tool problem. Cheers, Nicola Il 08.05.2015 10:44 Christian Schudoma (TSL) ha scritto: Hi all, I have encountered a problem when trying to run trinityrnaseq (Galaxy Tool Version 0.0.1) from Galaxy. Leaving the strand-specificity input parameter as None will prevent the form from being submitted. Instead, the strand-specificity input box will be highlighted in red and I'm asked to Please verify this parameter. Before the last update we were running a very very old instance of Galaxy (I think the update before the last was in 2013) from which we could submit trinity-jobs just fine. I found a commit from Aysam from late 2014 which does something in the immediate vicinity of the Please verify this parameter - message. (https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/ [1]), which I am guessing could have something to do with it. Anyone got any ideas regarding this? Any help would be appreciated. Thanks Christian -- Dr. Christian Schudoma Bioinformatics Support Officer Bioinformatics Group The Sainsbury Laboratory Norwich Research Park Norwich NR4 7UH United Kingdom ** +44 (0) 1603 450 601 christian.schud...@tsl.ac.uk [2] twitter: @cpt_bwt Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] trinity tool form not allowing None input for strand-specificity
The problem is not in the Cheetah code, which does not get executed because of the validation error. I think this a Galaxy bug which tries to validate the parameter values but interprets the value None of the library_type param as no option selected. Nicola Il 08.05.2015 19:18 Christian Schudoma (TSL) ha scritto: Hi Nicola It happens with both versions available on the main toolshed. We originally had the package from bhaas, latest revision from 2012 and yesterday I installed the one from biomonika which requires package_trinityrnaseq_2013_08_14 (which in turn downloads a copy of trinity). Both have the same problem. Since a None value for the strand-spec. parameter means that the parameter is ignored (in the Cheetah code) I would think that the issue does not go down to the tool level (I can run Trinity on the command line just fine without specifying the strand-spec.) Thanks Christian On 08/05/15 17:51, Nicola Soranzo wrote: Hi Christian, was the trinityrnaseq tool installed from the Tool Shed? Which repository? Just to check this is not a tool problem. Cheers, Nicola Il 08.05.2015 10:44 Christian Schudoma (TSL) ha scritto: Hi all, I have encountered a problem when trying to run trinityrnaseq (Galaxy Tool Version 0.0.1) from Galaxy. Leaving the strand-specificity input parameter as None will prevent the form from being submitted. Instead, the strand-specificity input box will be highlighted in red and I'm asked to Please verify this parameter. Before the last update we were running a very very old instance of Galaxy (I think the update before the last was in 2013) from which we could submit trinity-jobs just fine. I found a commit from Aysam from late 2014 which does something in the immediate vicinity of the Please verify this parameter - message. (https://bitbucket.org/galaxy/galaxy-central/commits/bda732e549b7/ [1]), which I am guessing could have something to do with it. Anyone got any ideas regarding this? Any help would be appreciated. Thanks Christian -- Dr. Christian Schudoma Bioinformatics Support Officer Bioinformatics Group The Sainsbury Laboratory Norwich Research Park Norwich NR4 7UH United Kingdom ** +44 (0) 1603 450 601 christian.schud...@tsl.ac.uk [2] twitter: @cpt_bwt Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l'app Vai su https://www.indoona.com/ [3] Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo. E chiami gratis anche i numeri fissi e mobili nel mondo! Scarica subito l’app Vai su https://www.indoona.com/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
