Hi, I was wondering if I could get some more information on how the <repeat> tag works. If I am repeating an argument, say "$samplename," would the xml file just pass extra arguments to my command line, or do I have to do some extra configuration? If it is passing extra arguments, are they lumped together? For example if I want to repeat both $samplename and $lane using the same tag, is it sending to the command line $samplename1 $samplename2 $samplename3 $lane1 $lane2 $lane3 or $samplename1 $lane1 $samplename2 $lane2 $samplename3 $lane3? What types are supported by the <repeat> tag? Currently I am using type="text" but this does not seem to be working. Thanks!
When I have used repeats in the passed, I have used Cheetah templating in either a <configfile> or in the <command>. The cheetah manual is at http://www.cheetahtemplate.org/. In my case, I usually loop over the items in the repeat as shown below: <repeat name="my_repeat"> #for $i, $my_repeat in enumerate( $my_repeats ) $my_repeat.repeated_value #end for On Thu, Jul 8, 2010 at 10:43 AM, Pei, Bing <Pei.Bing@mayo.edu> wrote:
Hi,
I was wondering if I could get some more information on how the <repeat> tag works. If I am repeating an argument, say "$samplename," would the xml file just pass extra arguments to my command line, or do I have to do some extra configuration? If it is passing extra arguments, are they lumped together? For example if I want to repeat both $samplename and $lane using the same tag, is it sending to the command line $samplename1 $samplename2 $samplename3 $lane1 $lane2 $lane3 or $samplename1 $lane1 $samplename2 $lane2 $samplename3 $lane3? What types are supported by the <repeat> tag? Currently I am using type="text" but this does not seem to be working.
Thanks!
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123 jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann
Whoops, accidentally sent that early. Edited below On Fri, Jul 9, 2010 at 8:37 AM, Jesse Erdmann <jerdmann@umn.edu> wrote:
When I have used repeats in the passed, I have used Cheetah templating in either a <configfile> or in the <command>. The cheetah manual is at http://www.cheetahtemplate.org/.
In my case, I usually loop over the items in the repeat as shown below:
<repeat name="my_repeat"> <param name="repeated_value"/> </repeat>
<command> #for $i, $my_repeat in enumerate( $my_repeats ) $my_repeat.repeated_value #end for </command>
On Thu, Jul 8, 2010 at 10:43 AM, Pei, Bing <Pei.Bing@mayo.edu> wrote:
Hi,
I was wondering if I could get some more information on how the <repeat> tag works. If I am repeating an argument, say "$samplename," would the xml file just pass extra arguments to my command line, or do I have to do some extra configuration? If it is passing extra arguments, are they lumped together? For example if I want to repeat both $samplename and $lane using the same tag, is it sending to the command line $samplename1 $samplename2 $samplename3 $lane1 $lane2 $lane3 or $samplename1 $lane1 $samplename2 $lane2 $samplename3 $lane3? What types are supported by the <repeat> tag? Currently I am using type="text" but this does not seem to be working.
Thanks!
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123
jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann
-- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123 jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann
Hi, I want to ask if it is possible to evalute the value of some tool checkboxes within this cheetah templates. I want to do something like this. A certain tool has the ability to skip some test (e.g. --skipsomething). So I added a checkbox option for the user and depending of his selection the commandline should be: tool.py $input $output or tool.py $input --skipsomething $output <tool name="tool" id="tool"> <command interpreter="python"> tool.py $input #if $skip.value == "true" #--skipsomething #endif '$output' </command> <inputs> <param name="input" type="text" label="Full path to source file"/> <param name="skip" type="boolean" label="skip something"> </input> ... Or is there an easier way to achieve this without cheetah? Thx for help and haveaniceweekend ;-)
Try this: <command interpreter="python">tool.py #if $skip == True -skipsomething #endif $output </command> On Fri, Jul 9, 2010 at 10:46 AM, Michael Siebauer <michael_siebauer@eva.mpg.de> wrote:
Hi,
I want to ask if it is possible to evalute the value of some tool checkboxes within this cheetah templates. I want to do something like this.
A certain tool has the ability to skip some test (e.g. --skipsomething). So I added a checkbox option for the user and depending of his selection the commandline should be:
tool.py $input $output or tool.py $input --skipsomething $output
<tool name="tool" id="tool"> <command interpreter="python"> tool.py $input #if $skip.value == "true" #--skipsomething #endif '$output' </command> <inputs> <param name="input" type="text" label="Full path to source file"/> <param name="skip" type="boolean" label="skip something">
</input> ...
Or is there an easier way to achieve this without cheetah?
Thx for help and haveaniceweekend ;-)
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Jesse Erdmann Bioinformatics Analyst Masonic Cancer Center University of Minnesota jerdmann@umn.edu 612-626-3123 jesse@jesseerdmann.com Twitter: http://twitter.com/jesseerdmann
That doesnt seem to work, regardless wheter the chechbox is checked or not, the if condition is always evaluated as true. :-/ As a workaround I use now: <param name="skip" type="boolean" label="skip something" truevalue="--skipsomething" falsevalue=""> But it would be way nicer if could manage to use if conditions. Am 09.07.2010 18:22, schrieb Jesse Erdmann:
Try this:
<command interpreter="python">tool.py #if $skip == True -skipsomething #endif $output </command>
On Fri, Jul 9, 2010 at 10:46 AM, Michael Siebauer <michael_siebauer@eva.mpg.de> wrote:
Hi,
I want to ask if it is possible to evalute the value of some tool checkboxes within this cheetah templates. I want to do something like this.
A certain tool has the ability to skip some test (e.g. --skipsomething). So I added a checkbox option for the user and depending of his selection the commandline should be:
tool.py $input $output or tool.py $input --skipsomething $output
<tool name="tool" id="tool"> <command interpreter="python"> tool.py $input #if $skip.value == "true" #--skipsomething #endif '$output' </command> <inputs> <param name="input" type="text" label="Full path to source file"/> <param name="skip" type="boolean" label="skip something">
</input> ...
Or is there an easier way to achieve this without cheetah?
Thx for help and haveaniceweekend ;-)
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Michael, I think boolean parameters require you to set truevalue and falsevalue if you're going to use them further in the xml file, so the way you're doing it now is correct. -Kanwei On Mon, Jul 12, 2010 at 5:23 AM, Michael Siebauer <michael_siebauer@eva.mpg.de> wrote:
That doesnt seem to work, regardless wheter the chechbox is checked or not, the if condition is always evaluated as true. :-/
As a workaround I use now:
<param name="skip" type="boolean" label="skip something" truevalue="--skipsomething" falsevalue="">
But it would be way nicer if could manage to use if conditions.
Am 09.07.2010 18:22, schrieb Jesse Erdmann:
Try this:
<command interpreter="python">tool.py #if $skip == True -skipsomething #endif $output </command>
On Fri, Jul 9, 2010 at 10:46 AM, Michael Siebauer <michael_siebauer@eva.mpg.de> wrote:
Hi,
I want to ask if it is possible to evalute the value of some tool checkboxes within this cheetah templates. I want to do something like this.
A certain tool has the ability to skip some test (e.g. --skipsomething). So I added a checkbox option for the user and depending of his selection the commandline should be:
tool.py $input $output or tool.py $input --skipsomething $output
<tool name="tool" id="tool"> <command interpreter="python"> tool.py $input #if $skip.value == "true" #--skipsomething #endif '$output' </command> <inputs> <param name="input" type="text" label="Full path to source file"/> <param name="skip" type="boolean" label="skip something">
</input> ...
Or is there an easier way to achieve this without cheetah?
Thx for help and haveaniceweekend ;-)
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
_______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Michael, I recently needed the same thing (checking the value of a checkbox inside cheetah code). After some tinkering, the way to do it is: <param name="skip" type="boolean" label="skip something"> <command> #if $skip.value == True: --skip-- #else --don't skip-- #end if </command> Note the '$skip.value' (and not just '$skip') which is a boolean (not a string). No need for 'truevalue' and 'falsevalue'. Regards, -gordon Kanwei Li wrote, On 07/12/2010 03:20 PM:
Hi Michael,
I think boolean parameters require you to set truevalue and falsevalue if you're going to use them further in the xml file, so the way you're doing it now is correct.
-Kanwei
On Mon, Jul 12, 2010 at 5:23 AM, Michael Siebauer <michael_siebauer@eva.mpg.de> wrote:
That doesnt seem to work, regardless wheter the chechbox is checked or not, the if condition is always evaluated as true. :-/
As a workaround I use now:
<param name="skip" type="boolean" label="skip something" truevalue="--skipsomething" falsevalue="">
But it would be way nicer if could manage to use if conditions.
Am 09.07.2010 18:22, schrieb Jesse Erdmann:
Try this:
<command interpreter="python">tool.py #if $skip == True -skipsomething #endif $output </command>
On Fri, Jul 9, 2010 at 10:46 AM, Michael Siebauer <michael_siebauer@eva.mpg.de> wrote:
Hi,
I want to ask if it is possible to evalute the value of some tool checkboxes within this cheetah templates. I want to do something like this.
A certain tool has the ability to skip some test (e.g. --skipsomething). So I added a checkbox option for the user and depending of his selection the commandline should be:
tool.py $input $output or tool.py $input --skipsomething $output
<tool name="tool" id="tool"> <command interpreter="python"> tool.py $input #if $skip.value == "true" #--skipsomething #endif '$output' </command> <inputs> <param name="input" type="text" label="Full path to source file"/> <param name="skip" type="boolean" label="skip something">
</input> ...
Or is there an easier way to achieve this without cheetah?
Thx for help and haveaniceweekend ;-)
participants (5)
-
Assaf Gordon -
Jesse Erdmann -
Kanwei Li -
Michael Siebauer -
Pei, Bing