Re: [galaxy-dev] Tools: dynamic check of file type?
That's exactly what I meant. I've been searching for a way to achieve this otherwise but I didn't find any idea. Does anyone have one? L-A Le 20/05/2011 15:49, Peter Cock a écrit : 2011/5/20 Louise-Amélie Schmitt: 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 and 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] Tools: dynamic check of file type?
2011/5/20 Louise-Amélie Schmitt : > 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 and 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] 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 Schmitt: 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?
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 Schmitt: 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/
Re: [galaxy-dev] Tools: dynamic check of file type?
2011/5/20 Louise-Amélie Schmitt : > 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/
[galaxy-dev] Tools: dynamic check of file type?
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? Regards, L-A ___ 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/