Choosing between pre-existing file or user-defined file as tool input
Hello, I am building a new tool for Galaxy and I would like for it to have an option for the user to choose his file for input or to use a pre-installed file on the server (in a specific path not defined by the user). Can anyone tell me which is the right parameter type to use in the configuration file? Thank you in advance, Makis Ladoukakis
On Mon, Sep 17, 2012 at 1:21 PM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Hello,
I am building a new tool for Galaxy and I would like for it to have an option for the user to choose his file for input or to use a pre-installed file on the server (in a specific path not defined by the user). Can anyone tell me which is the right parameter type to use in the configuration file?
Thank you in advance, Makis Ladoukakis
The *.loc file mechanism might be a good choice. The BLAST+ wrapper do this to offer you a choice of your own database file from the history, or a system provided database like NR. The associated *.loc file is a simple tabular file of available BLAST databases, and must be filled in by the local Galaxy administrator. Peter
Dear Peter, Thank you for your help. I have used the blastp.loc file and renamed it and altered it in order to keep the same format as in the previous tool. Also I used the same ordering from blastp tool (i.e. 0=value 1=name 2=path). Nevertheless when I run my tool I get the error: Error: Failed to open txt file test_17_Sep_2012 for reading. I have used chmod 777 for my file but the issue still persists. Can you help me please? What could be the problem. Thank you in advance, Makis Ladoukakis
Date: Mon, 17 Sep 2012 13:30:34 +0100 Subject: Re: [galaxy-dev] Choosing between pre-existing file or user-defined file as tool input From: p.j.a.cock@googlemail.com To: makis4ever@hotmail.com CC: galaxy-dev@lists.bx.psu.edu
On Mon, Sep 17, 2012 at 1:21 PM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Hello,
I am building a new tool for Galaxy and I would like for it to have an option for the user to choose his file for input or to use a pre-installed file on the server (in a specific path not defined by the user). Can anyone tell me which is the right parameter type to use in the configuration file?
Thank you in advance, Makis Ladoukakis
The *.loc file mechanism might be a good choice. The BLAST+ wrapper do this to offer you a choice of your own database file from the history, or a system provided database like NR. The associated *.loc file is a simple tabular file of available BLAST databases, and must be filled in by the local Galaxy administrator.
Peter
On Mon, Sep 17, 2012 at 2:44 PM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Dear Peter,
Thank you for your help. I have used the blastp.loc file and renamed it and altered it in order to keep the same format as in the previous tool. Also I used the same ordering from blastp tool (i.e. 0=value 1=name 2=path). Nevertheless when I run my tool I get the error:
Error: Failed to open txt file test_17_Sep_2012 for reading.
I have used chmod 777 for my file but the issue still persists. Can you help me please? What could be the problem.
Thank you in advance, Makis Ladoukakis
It would probably help to see your tool's XML file. Are you using a public source code repository during development? If you are manually installing the tool (which is how I work when developing a new tool), the *.loc files need to go in the folder galaxy/tool-data - but this is probably a bit different via a ToolShed installation. Also note that (currently) you must restart Galaxy in order for any changes to the *.loc files to take effect: https://bitbucket.org/galaxy/galaxy-central/issue/538/ Peter
participants (2)
-
Makis Ladoukakis -
Peter Cock