Jelle,
(I've copied this to galaxy-dev since it's more appropriate to that one)
The data table approach is fairly new, so there aren't too many examples yet, although more tools are being converted and will be available soon in the distribution. Basically, there are 3 steps to using it: 1. Modify tool_data_table_conf.xml to specify: - the bowtie data table - the column types in the loc file - It should look something like this: <table name="bowtie_indexes"> <columns>name, value</columns> <file path="tool-data/bowtie_indices.loc" /> </table> 2. Create/modify the loc file to correspond with the column types specified in tool_data_table_conf.xml (in this example, the loc file doesn't have to be changed), though we are going to be changing the specification to <columns>value, dbkey, name, path</columns> 3. Modify the Bowtie wrapper to use the data table instead of the loc file directly, replacing this: <options from_file="bowtie_indices.loc"> <column name="value" index="1" /> <column name="name" index="0" /> </options> - with this: <options from_data_table="bowtie_indexes"/>
The <actions> in the Bowtie wrapper is used in lieu of the deprecated <code> tag to set the dbkey of the output dataset. In bowtie_wrapper.xml, according to the first action block, if the refGenomeSource.genomeSource is "indexed" (not "history"), then it will assign the dbkey of the output file to be the same as that of the reference file. It does this by looking at through the loc file and finding the line that has the value that's been selected in the index dropdown box as column 1 of the loc file entry and using the dbkey, in column 0 (ignoring comment lines (starting with #) along the way).
If refGenomeSource.genomeSource is "history", it resorts to default behavior for Galaxy, which is that the output is assigned the same value as the first input that has a dbkey specified.
The second block would not be needed for most cases--it is required here to handle the specific case of a small reference file we use for functional testing. It says that if the dbkey has been set to "equCab2chrM" (that's what the <filter type="metadata_value"... column="1" /> tag) does then it should be changed to "equCab2" (the <option type="from_param" ... column="0" ...> tag does).
If you need more information than this, let us know.
Regards, Kelly
On Oct 1, 2010, at 4:22 AM, Jelle Scholtalbers wrote:
Hey,
I was looking through the bowtie_wrapper.xml to get some information about how to use the tool_data_table_conf.xml. There I also noticed in the output section the tag <actions>. Is there any information on this tag as is does seem to be used a lot?
Cheers, Jelle _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi Kelly,
thank you. I added this info also to the wiki for further reference.
Cheers, Jelle
On Fri, Oct 1, 2010 at 6:07 PM, Kelly Vincent kpvincent@bx.psu.edu wrote:
Jelle,
(I've copied this to galaxy-dev since it's more appropriate to that one)
The data table approach is fairly new, so there aren't too many examples yet, although more tools are being converted and will be available soon in the distribution. Basically, there are 3 steps to using it:
- Modify tool_data_table_conf.xml to specify:
- the bowtie data table - the column types in the loc file - It should look something like this: <table name="bowtie_indexes"> <columns>name, value</columns> <file path="tool-data/bowtie_indices.loc" /> </table> 2. Create/modify the loc file to correspond with the column types specified in tool_data_table_conf.xml (in this example, the loc file doesn't have to be changed), though we are going to be changing the specification to <columns>value, dbkey, name, path</columns> 3. Modify the Bowtie wrapper to use the data table instead of the loc file directly, replacing this: <options from_file="bowtie_indices.loc"> <column name="value" index="1" /> <column name="name" index="0" /> </options> - with this: <options from_data_table="bowtie_indexes"/>
The <actions> in the Bowtie wrapper is used in lieu of the deprecated <code> tag to set the dbkey of the output dataset. In bowtie_wrapper.xml, according to the first action block, if the refGenomeSource.genomeSource is "indexed" (not "history"), then it will assign the dbkey of the output file to be the same as that of the reference file. It does this by looking at through the loc file and finding the line that has the value that's been selected in the index dropdown box as column 1 of the loc file entry and using the dbkey, in column 0 (ignoring comment lines (starting with #) along the way).
If refGenomeSource.genomeSource is "history", it resorts to default behavior for Galaxy, which is that the output is assigned the same value as the first input that has a dbkey specified.
The second block would not be needed for most cases--it is required here to handle the specific case of a small reference file we use for functional testing. It says that if the dbkey has been set to "equCab2chrM" (that's what the <filter type="metadata_value"... column="1" /> tag) does then it should be changed to "equCab2" (the <option type="from_param" ... column="0" ...> tag does).
If you need more information than this, let us know.
Regards, Kelly
On Oct 1, 2010, at 4:22 AM, Jelle Scholtalbers wrote:
Hey,
I was looking through the bowtie_wrapper.xml to get some information about how to use the tool_data_table_conf.xml. There I also noticed in the output section the tag <actions>. Is there any information on this tag as is does seem to be used a lot?
Cheers, Jelle _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
galaxy-dev@lists.galaxyproject.org
-
Jelle Scholtalbers -
Kelly Vincent