planemo test with <options from_data_table>
Hi galaxy-dev, I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo: 'Error creating a job for these tool inputs - Parameter refGenomeSource_type requires a value, but has no legal values defined.\n
From my script XML:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test" (mirrored)
<table name="type_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, name, path</columns> <file path="tool-data/twobit.loc" /> </table>
and from twobit.loc (where the columns are tab separated):
hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Any suggestions would be greatly appreciated!
Hi DK, Looking at your XML that looks OK. It might not be important, but how exactly are you running planemo test? I'm asking because currently it will not create tool-data/twobit.loc for you from your sample file - although in that case I would have expected a different error message: https://github.com/galaxyproject/planemo/issues/530 https://github.com/galaxyproject/planemo/issues/530 Is planemo lint happy with your tool? Peter On Thu, Oct 6, 2016 at 11:08 PM, D K <danielfortin86@gmail.com> wrote:
Hi galaxy-dev,
I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo:
'Error creating a job for these tool inputs - Parameter refGenomeSource_type requires a value, but has no legal values defined.\n
From my script XML:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test" (mirrored)
<table name="type_indexes" comment_char="#" allow_duplicate_entries=" False"> <columns>value, name, path</columns> <file path="tool-data/twobit.loc" /> </table>
and from twobit.loc (where the columns are tab separated):
hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/ reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Any suggestions would be greatly appreciated!
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Hi Peter, This is the command I'm using to run planemo: . galaxy_test/.venv/bin/activate planemo test --test_data /home/galaxy-functional-testdata --galaxy_root galaxy-test/ --skip_venv test.xml I'm getting no errors when using the planemo lint tool. Thanks! On Fri, Oct 7, 2016 at 2:06 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi DK,
Looking at your XML that looks OK.
It might not be important, but how exactly are you running planemo test?
I'm asking because currently it will not create tool-data/twobit.loc for you from your sample file - although in that case I would have expected a different error message:
https://github.com/galaxyproject/planemo/issues/530 https://github.com/galaxyproject/planemo/issues/530
Is planemo lint happy with your tool?
Peter
On Thu, Oct 6, 2016 at 11:08 PM, D K <danielfortin86@gmail.com> wrote:
Hi galaxy-dev,
I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo:
'Error creating a job for these tool inputs - Parameter refGenomeSource_type requires a value, but has no legal values defined.\n
From my script XML:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test" (mirrored)
<table name="type_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, name, path</columns> <file path="tool-data/twobit.loc" /> </table>
and from twobit.loc (where the columns are tab separated):
hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/refer ence_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Any suggestions would be greatly appreciated!
___________________________________________________________ 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/
Hi D K, for a good example of how to test parameters from data tables, please see: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrap... Your tool_data_table_conf.xml.test should be different from your .sample and contain: <file path="${__HERE__}/test-data/twobit.loc" /> Please note the use of ${__HERE__} to indicate the directory where the tool is. You should also have a comment-only tool-data/twobit.loc.sample , while the loc file for testing should be in test-data/twobit.loc Cheers, Nicola On 06/10/16 23:08, D K wrote:
Hi galaxy-dev,
I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo: 'Error creating a job for these tool inputs - Parameter refGenomeSource_type requires a value, but has no legal values defined.\n
From my script XML:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test" (mirrored)
<table name="type_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, name, path</columns> <file path="tool-data/twobit.loc" /> </table>
and from twobit.loc (where the columns are tab separated):
hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Any suggestions would be greatly appreciated!
___________________________________________________________ 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/
Hi Nicola, Thanks for the response, I'm still getting the same issue though. I've followed the set up you've shown for bowtie_wrappers but am getting the same error. I've changed my file structure to look like this: tmp/test.xml:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
tmp/tool_data_table_conf.xml.sample:
<tables> <table name="twobit_indexes" comment_char="#"> <columns>value, path</columns> <file path="tool-data/twobit.loc" /> </table> </tables>
tmp/tool_data_table_conf.xml.test:
<tables> <!-- Locations of indexes in the 2bit format --> <table name="twobit" comment_char="#" allow_duplicate_entries="False"> <columns>value, path</columns> <file path="${__HERE__}/test-data/twobit.loc" /> </table> </tables>
tmp/tool-data/twobit.loc
hsapiens /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
tmp/tool-data/twobit.loc
#
tmp/test-data/twobit.loc
hsapiens /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Rather than placing these twobit.loc files etc... under tmp with test.xml I've also tried putting these files under galaxy-test/tool-data, test-data, etc... and that didn't help either. I'm not understanding what I'm doing wrong here. Any additional suggestions would be appreciated. Thanks! On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo <nsoranzo@tiscali.it> wrote:
Hi D K, for a good example of how to test parameters from data tables, please see: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_ wrappers
Your tool_data_table_conf.xml.test should be different from your .sample and contain:
<file path="${__HERE__}/test-data/twobit.loc" />
Please note the use of ${__HERE__} to indicate the directory where the tool is. You should also have a comment-only tool-data/twobit.loc.sample , while the loc file for testing should be in test-data/twobit.loc
Cheers, Nicola
On 06/10/16 23:08, D K wrote:
Hi galaxy-dev,
I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo:
'Error creating a job for these tool inputs - Parameter refGenomeSource_type requires a value, but has no legal values defined.\n
From my script XML:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test" (mirrored)
<table name="type_indexes" comment_char="#" allow_duplicate_entries=" False"> <columns>value, name, path</columns> <file path="tool-data/twobit.loc" /> </table>
and from twobit.loc (where the columns are tab separated):
hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/ reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Any suggestions would be greatly appreciated!
___________________________________________________________ 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/
Hi D K, I think that the problem may be that the table name is different in your test.xml , tool_data_table_conf.xml.sample and tool_data_table_conf.xml.test files (type_indexes, twobit_indexes and twobit respectively), should always be twobit. Cheers, Nicola On 07/10/16 18:04, D K wrote:
Hi Nicola,
Thanks for the response, I'm still getting the same issue though. I've followed the set up you've shown for bowtie_wrappers but am getting the same error. I've changed my file structure to look like this:
tmp/test.xml:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
tmp/tool_data_table_conf.xml.sample:
<tables> <table name="twobit_indexes" comment_char="#"> <columns>value, path</columns> <file path="tool-data/twobit.loc" /> </table> </tables>
tmp/tool_data_table_conf.xml.test:
<tables> <!-- Locations of indexes in the 2bit format --> <table name="twobit" comment_char="#" allow_duplicate_entries="False"> <columns>value, path</columns> <file path="${__HERE__}/test-data/twobit.loc" /> </table> </tables>
tmp/tool-data/twobit.loc
hsapiens /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
tmp/tool-data/twobit.loc
#
tmp/test-data/twobit.loc
hsapiens /nfs/seqdata/reference_genome/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Rather than placing these twobit.loc files etc... under tmp with test.xml I've also tried putting these files under galaxy-test/tool-data, test-data, etc... and that didn't help either.
I'm not understanding what I'm doing wrong here. Any additional suggestions would be appreciated.
Thanks!
On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo <nsoranzo@tiscali.it <mailto:nsoranzo@tiscali.it>> wrote:
Hi D K, for a good example of how to test parameters from data tables, please see: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrap... <https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie_wrappers>
Your tool_data_table_conf.xml.test should be different from your .sample and contain:
<file path="${__HERE__}/test-data/twobit.loc" />
Please note the use of ${__HERE__} to indicate the directory where the tool is. You should also have a comment-only tool-data/twobit.loc.sample , while the loc file for testing should be in test-data/twobit.loc
Cheers, Nicola
On 06/10/16 23:08, D K wrote:
Hi galaxy-dev,
I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo: 'Error creating a job for these tool inputs - Parameter refGenomeSource_type requires a value, but has no legal values defined.\n
From my script XML:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test" (mirrored)
<table name="type_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, name, path</columns> <file path="tool-data/twobit.loc" /> </table>
and from twobit.loc (where the columns are tab separated):
hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/reference_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Any suggestions would be greatly appreciated!
___________________________________________________________ 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/ <https://lists.galaxyproject.org/>
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ <http://galaxyproject.org/search/mailinglists/>
Thanks Nicola, That fixed it when all of the files are in the tmp/ directory Is this file/directory structure required when doing this? When I try putting the relevant entries in "galaxy-test/tool_data_table_conf.xml.test" and "galaxy-test/tool_data_table_conf.xml.sample" and the "twobit.loc" in "galaxy-test/test-data" and "galaxy-test/tool-data" then I get the same error again. I'd like to be able to put the files here instead of in their own directory structure. Thanks! On Fri, Oct 7, 2016 at 10:04 AM, D K <danielfortin86@gmail.com> wrote:
Hi Nicola,
Thanks for the response, I'm still getting the same issue though. I've followed the set up you've shown for bowtie_wrappers but am getting the same error. I've changed my file structure to look like this:
tmp/test.xml:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
tmp/tool_data_table_conf.xml.sample:
<tables> <table name="twobit_indexes" comment_char="#"> <columns>value, path</columns> <file path="tool-data/twobit.loc" /> </table> </tables>
tmp/tool_data_table_conf.xml.test:
<tables> <!-- Locations of indexes in the 2bit format --> <table name="twobit" comment_char="#" allow_duplicate_entries=" False"> <columns>value, path</columns> <file path="${__HERE__}/test-data/twobit.loc" /> </table> </tables>
tmp/tool-data/twobit.loc
hsapiens /nfs/seqdata/reference_genome/ MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
tmp/tool-data/twobit.loc
#
tmp/test-data/twobit.loc
hsapiens /nfs/seqdata/reference_genome/ MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Rather than placing these twobit.loc files etc... under tmp with test.xml I've also tried putting these files under galaxy-test/tool-data, test-data, etc... and that didn't help either.
I'm not understanding what I'm doing wrong here. Any additional suggestions would be appreciated.
Thanks!
On Fri, Oct 7, 2016 at 3:26 AM, Nicola Soranzo <nsoranzo@tiscali.it> wrote:
Hi D K, for a good example of how to test parameters from data tables, please see: https://github.com/galaxyproject/tools-devteam/tree/master/ tools/bowtie_wrappers
Your tool_data_table_conf.xml.test should be different from your .sample and contain:
<file path="${__HERE__}/test-data/twobit.loc" />
Please note the use of ${__HERE__} to indicate the directory where the tool is. You should also have a comment-only tool-data/twobit.loc.sample , while the loc file for testing should be in test-data/twobit.loc
Cheers, Nicola
On 06/10/16 23:08, D K wrote:
Hi galaxy-dev,
I'm having a problem running a test using planemo where I would like the value of a parameter taken from one of the data tables. I get the following error in planemo:
'Error creating a job for these tool inputs - Parameter refGenomeSource_type requires a value, but has no legal values defined.\n
From my script XML:
<param name="refGenomeSource_type" type="select" label="Select a reference genome / transcriptome"> <options from_data_table="type_indexes"> </options> </param> ... <tests> <test> <param name="refGenomeSource_type" value="hsapiens"/> </test> </tests>
From my "tool_data_table_conf.xml.sample" and "tool_data_table_conf.xml.test" (mirrored)
<table name="type_indexes" comment_char="#" allow_duplicate_entries="False"> <columns>value, name, path</columns> <file path="tool-data/twobit.loc" /> </table>
and from twobit.loc (where the columns are tab separated):
hsapiens H. sapiens (hg38) /remote/RMS/users/galaxy/refer ence_genomes/MFEprimer_index/Homo_sapiens.GRCh38.cdna.all.fa
Any suggestions would be greatly appreciated!
___________________________________________________________ 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/
participants (3)
-
D K -
Nicola Soranzo -
Peter Cock