Hello,
I've been working with a local installation of Galaxy and my question is about how Galaxy chooses which file to use in the next step of the workflow.
I have created a custom file type called "cub" which is required for my custom tools and I have added this custom file type into the extension list. When I run the first step of my workflow, Galaxy will create an intermediate cub file called dataset_51.dat.cub containing my processed data, but also an empty intermediate dat file as well of the same name sans cub extension (dataset_51.dat) . The next tool in the workflow requires a cub file type input, but instead of using the cub file, it chooses to process the empty .dat file instead, causing the tool to process incorrectly.
I've looked over some settings and double checked that my tool xml files specify cub as the output file type and as the input file type for the next tool, but now I am at a loss. Is there anyway to specify to Galaxy that the cub file should be used in the next step of the workflow instead of the dat file?
Thank you very much for your help,
Kolby
On Sun, Jan 27, 2013 at 10:26 PM, Kolby Chien kc452@nau.edu wrote:
Hello,
I've been working with a local installation of Galaxy and my question is about how Galaxy chooses which file to use in the next step of the workflow.
I have created a custom file type called "cub" which is required for my custom tools and I have added this custom file type into the extension list. When I run the first step of my workflow, Galaxy will create an intermediate cub file called dataset_51.dat.cub containing my processed data, but also an empty intermediate dat file as well of the same name sans cub extension (dataset_51.dat) . The next tool in the workflow requires a cub file type input, but instead of using the cub file, it chooses to process the empty .dat file instead, causing the tool to process incorrectly.
I've looked over some settings and double checked that my tool xml files specify cub as the output file type and as the input file type for the next tool, but now I am at a loss. Is there anyway to specify to Galaxy that the cub file should be used in the next step of the workflow instead of the dat file?
Galaxy wants all the files to use the names Galaxy tells the tool, and those filenames all end with .dat - the problem is probably Galaxy has told you (i.e. your tool) to use dataset_51.dat as the output file, but your tool has instead used dataset_51.dat.cub (which Galaxy will ignore).
Peter
You can work around this using the from_work_dir attribute when specifying the output file in your tool config.
-- jt
(composed on my phone)
On Jan 27, 2013, at 6:13 PM, Peter Cock p.j.a.cock@googlemail.com wrote:
On Sun, Jan 27, 2013 at 10:26 PM, Kolby Chien kc452@nau.edu wrote:
Hello,
I've been working with a local installation of Galaxy and my question is about how Galaxy chooses which file to use in the next step of the workflow.
I have created a custom file type called "cub" which is required for my custom tools and I have added this custom file type into the extension list. When I run the first step of my workflow, Galaxy will create an intermediate cub file called dataset_51.dat.cub containing my processed data, but also an empty intermediate dat file as well of the same name sans cub extension (dataset_51.dat) . The next tool in the workflow requires a cub file type input, but instead of using the cub file, it chooses to process the empty .dat file instead, causing the tool to process incorrectly.
I've looked over some settings and double checked that my tool xml files specify cub as the output file type and as the input file type for the next tool, but now I am at a loss. Is there anyway to specify to Galaxy that the cub file should be used in the next step of the workflow instead of the dat file?
Galaxy wants all the files to use the names Galaxy tells the tool, and those filenames all end with .dat - the problem is probably Galaxy has told you (i.e. your tool) to use dataset_51.dat as the output file, but your tool has instead used dataset_51.dat.cub (which Galaxy will ignore).
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:
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James Taylor -
Kolby Chien -
Peter Cock