Re: [galaxy-dev] Set a new metadata attribute
Hi Nikos As a 'quick and dirty' work-around, I suggest generating in addition to the output file a 'log' file, which can be read by the subsequent tool. Hans-Rudolf On 09/26/2014 04:54 PM, Peter Cock wrote: On Fri, Sep 26, 2014 at 3:01 PM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi all, In a tool that I am writting I want to pass an input parameter value (string) into the output file's metadata. Meaning that one of the tool parameters is a barcode signature, 'NNWTGXN' for example. I want that attribute to be stored somehow in the output file in order to be read by a subsequent tool without the user having to set that parameter again. The files I'll be working with are in FASTQ, BAM and tabular format. Is it possible? Bests, Nikos Your code can write the value directly into an output file (e.g. one of the SAM/BAM headers might work), but I don't think there is anything suitable within Galaxy for re-exporting the parameter value as an input parameter for a future tool. However, at the workflow level you can set variables - might that be a way forward? https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit 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: http://lists.bx.psu.edu/ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Set a new metadata attribute
Hi all, In a tool that I am writting I want to pass an input parameter value (string) into the output file's metadata. Meaning that one of the tool parameters is a barcode signature, 'NNWTGXN' for example. I want that attribute to be stored somehow in the output file in order to be read by a subsequent tool without the user having to set that parameter again. The files I'll be working with are in FASTQ, BAM and tabular format. Is it possible? Bests, Nikos ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Set a new metadata attribute
On Fri, Sep 26, 2014 at 3:01 PM, Nikos Sidiropoulos nikos.sid...@gmail.com wrote: Hi all, In a tool that I am writting I want to pass an input parameter value (string) into the output file's metadata. Meaning that one of the tool parameters is a barcode signature, 'NNWTGXN' for example. I want that attribute to be stored somehow in the output file in order to be read by a subsequent tool without the user having to set that parameter again. The files I'll be working with are in FASTQ, BAM and tabular format. Is it possible? Bests, Nikos Your code can write the value directly into an output file (e.g. one of the SAM/BAM headers might work), but I don't think there is anything suitable within Galaxy for re-exporting the parameter value as an input parameter for a future tool. However, at the workflow level you can set variables - might that be a way forward? https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
