Trouble getting setting dbkey of output data
I am having trouble setting the dbkey of an output data set. The input and output, respectively, is shown below. I copied this from the bowtie_wrapper.xml but the difference is that I do not have a condition on selecting the reference genome. My tool requires a .loc file. The tools completes correctly but the dbkey is not set. Any thoughts on what I may be doing wrong? Thanks, Ilya <param name="input2" type="select" label="Select a reference genome"> <options from_data_table="RNASEQ_contams"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available for the selected input dataset" /> </options> </param> <data format="sam" name="output2" label="${tool.name} on ${on_string}:Output Sam File" /> <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="RNASEQ_contams" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="input2" column="0"/> </option> </action> </actions> Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>
Anybody, anybody? Thanks, Ilya From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Monday, October 17, 2011 9:31 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Trouble getting setting dbkey of output data I am having trouble setting the dbkey of an output data set. The input and output, respectively, is shown below. I copied this from the bowtie_wrapper.xml but the difference is that I do not have a condition on selecting the reference genome. My tool requires a .loc file. The tools completes correctly but the dbkey is not set. Any thoughts on what I may be doing wrong? Thanks, Ilya <param name="input2" type="select" label="Select a reference genome"> <options from_data_table="RNASEQ_contams"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available for the selected input dataset" /> </options> </param> <data format="sam" name="output2" label="${tool.name} on ${on_string}:Output Sam File" /> <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="RNASEQ_contams" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="input2" column="0"/> </option> </action> </actions> Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>
Hi Ilya, The 'actions' tagset must be within the ''data' tagset, you have it outside. Try something like: <data format="sam" name="output2" label="${tool.name} on ${on_string}:Output Sam File" > <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="RNASEQ_contams" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="input2" column="0"/> </option> </action> </actions> </data> Please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Oct 18, 2011, at 12:29 PM, Chorny, Ilya wrote:
Anybody, anybody?
Thanks,
Ilya
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Chorny, Ilya Sent: Monday, October 17, 2011 9:31 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Trouble getting setting dbkey of output data
I am having trouble setting the dbkey of an output data set. The input and output, respectively, is shown below. I copied this from the bowtie_wrapper.xml but the difference is that I do not have a condition on selecting the reference genome. My tool requires a .loc file. The tools completes correctly but the dbkey is not set. Any thoughts on what I may be doing wrong?
Thanks,
Ilya
<param name="input2" type="select" label="Select a reference genome"> <options from_data_table="RNASEQ_contams"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available for the selected input dataset" /> </options> </param>
<data format="sam" name="output2" label="${tool.name} on ${on_string}:Output Sam File" /> <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="RNASEQ_contams" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="input2" column="0"/> </option> </action> </actions>
Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com Website: www.illumina.com
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Great, thanks!!! From: Daniel Blankenberg [mailto:dan@bx.psu.edu] Sent: Tuesday, October 18, 2011 10:24 AM To: Chorny, Ilya Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Trouble getting setting dbkey of output data Hi Ilya, The 'actions' tagset must be within the ''data' tagset, you have it outside. Try something like: <data format="sam" name="output2" label="${tool.name} on ${on_string}:Output Sam File" > <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="RNASEQ_contams" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="input2" column="0"/> </option> </action> </actions> </data> Please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Oct 18, 2011, at 12:29 PM, Chorny, Ilya wrote: Anybody, anybody? Thanks, Ilya From: galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [mailto:galaxy-dev-bounces@lists.bx.psu.edu]<mailto:[mailto:galaxy-dev-bounces@lists.bx.psu.edu]> On Behalf Of Chorny, Ilya Sent: Monday, October 17, 2011 9:31 AM To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Trouble getting setting dbkey of output data I am having trouble setting the dbkey of an output data set. The input and output, respectively, is shown below. I copied this from the bowtie_wrapper.xml but the difference is that I do not have a condition on selecting the reference genome. My tool requires a .loc file. The tools completes correctly but the dbkey is not set. Any thoughts on what I may be doing wrong? Thanks, Ilya <param name="input2" type="select" label="Select a reference genome"> <options from_data_table="RNASEQ_contams"> <filter type="sort_by" column="2" /> <validator type="no_options" message="No indexes are available for the selected input dataset" /> </options> </param> <data format="sam" name="output2" label="${tool.name} on ${on_string}:Output Sam File" /> <actions> <action type="metadata" name="dbkey"> <option type="from_data_table" name="RNASEQ_contams" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="input2" column="0"/> </option> </action> </actions> Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.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: http://lists.bx.psu.edu/
participants (2)
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Chorny, Ilya -
Daniel Blankenberg