Re: [galaxy-dev] Tools: dynamic check of file type?
Well I'm still missing something... Is there a way to use the conditional tag sets in the tool's xml with it? To suppress the unnecessary options for a given file type? or more than one? regards, L-A Le 20/05/2011 13:15, Louise-Amélie Schmitt a écrit : It's exactly what I needed!!! Thanks a lot! L-A Le 20/05/2011 12:29, Peter Cock a écrit : 2011/5/20 Louise-Amélie Schmittlouise-amelie.schm...@embl.de: Hello Is there a way to check the file type with a conditional tag set within a tool? For example, if the tool can accept several file types but I have to make cheetah shut off some stuff for a couple of them? You can do conditional code in the cheetah template using $input.ext or $input.extension which both give you the Galaxy file type of an input file parameter called $input. For example, look at tools/fastx_toolkit/fastx_clipper.xml which does: #if $input.ext == fastqsanger: -Q 33 #end if Alternatively, if you want to do this in the script being called by Galaxy, just pass $input.ext as part of the command line. 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/ ___ 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/
Re: [galaxy-dev] Tools: dynamic check of file type?
2011/5/20 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Well I'm still missing something... Is there a way to use the conditional tag sets in the tool's xml with it? To suppress the unnecessary options for a given file type? or more than one? It sounds like you want to use the conditional and param tags, but rather than responding to another parameter directly (e.g. a select), you want to look at an input file parameter's file type? I don't know if that is possible, but I can thing of a couple of examples where I could use that functionality. 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/
Re: [galaxy-dev] Database query
Hi Harenda, I'll repeat what Hans has said - depending on what you're doing, this could cause issues. Depending on what you're doing, you may want to look at our user template functionality, if you're storing extra data about users. If it's best to use an extra column on the user table, you should be able to access that column by getting a user object in the interface and accessing the column as an attribute on the object: user = sa_session.query( galaxy.model.User ).get( user id ) user.new_column = value sa_session.add( user ) sa_session.flush() --nate Hans-Rudolf Hotz wrote: Hi Harendra Be very careful when you 'mess' with the database! And I would definitively refrain from changing the database schema, as this might very well cause problems in the future when you need to upgrade the schema as part of a Galaxy code update. If you really need a changed 'galaxy_user' table, I suggest to set up a second database with a copy of this table and change it there. And when ever you need to access the extra column, connect to the other database. Anyway, your actual question was how to add or modify data in a table? I am confused: you know the syntax for changing the schema of a table, but you don't know the syntax for manipulating the data of a table? You don't say, whether you are using PostgreSQL or MySQL, in case of MySQL, I recommend to read: http://dev.mysql.com/doc/refman/5.1/en/update.html http://dev.mysql.com/doc/refman/5.1/en/insert.html Regards, Hans On 05/20/2011 08:18 AM, Harendra chawla wrote: Hi everyone, I have a specific requirement in which I have changed the schema of one table in the database but I am not able find out the way to add the data into the table. Can anyone suggest where and how can i add or modify the data in the table. For example there is a table named galaxy_user, if I will add an extra column into that table then how and where can i add the data for that column?? Regards Harendra ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] Database query
Hi, Thanks a lot for the suggestion, I will try to convince my boss considering the issues stated by both of you. And thanks Nate for the syntax to add data. Regards Harendra On Fri, May 20, 2011 at 9:09 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Harenda, I'll repeat what Hans has said - depending on what you're doing, this could cause issues. Depending on what you're doing, you may want to look at our user template functionality, if you're storing extra data about users. If it's best to use an extra column on the user table, you should be able to access that column by getting a user object in the interface and accessing the column as an attribute on the object: user = sa_session.query( galaxy.model.User ).get( user id ) user.new_column = value sa_session.add( user ) sa_session.flush() --nate Hans-Rudolf Hotz wrote: Hi Harendra Be very careful when you 'mess' with the database! And I would definitively refrain from changing the database schema, as this might very well cause problems in the future when you need to upgrade the schema as part of a Galaxy code update. If you really need a changed 'galaxy_user' table, I suggest to set up a second database with a copy of this table and change it there. And when ever you need to access the extra column, connect to the other database. Anyway, your actual question was how to add or modify data in a table? I am confused: you know the syntax for changing the schema of a table, but you don't know the syntax for manipulating the data of a table? You don't say, whether you are using PostgreSQL or MySQL, in case of MySQL, I recommend to read: http://dev.mysql.com/doc/refman/5.1/en/update.html http://dev.mysql.com/doc/refman/5.1/en/insert.html Regards, Hans On 05/20/2011 08:18 AM, Harendra chawla wrote: Hi everyone, I have a specific requirement in which I have changed the schema of one table in the database but I am not able find out the way to add the data into the table. Can anyone suggest where and how can i add or modify the data in the table. For example there is a table named galaxy_user, if I will add an extra column into that table then how and where can i add the data for that column?? Regards Harendra ___ 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/ ___ 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/ ___ 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/
