Question about the <repeat> tag
Hello all, I have a question on how the <repeat> tag works in a Galaxy tool XML file. Right now I have a perl script that takes in various arguments. One of the arguments I have is a repeated one which is just a file selection feature. The script works something like this: script.pl $arg1 $arg2 $varyingNumOfArgs By using <repeat>, is the execution of the script something like this? script.pl $arg1 $arg2 $repeatedArg1 $repeatedArg2 ... $repeatedArgN where repeatedArgs1 ... repeatedArgsN are basically arguments specified by the <repeat> tag. If so, is there a certain way to access these repeated arguments and pass them into my script in the <command> tag? This is the part where I am not quite sure how <repeat> works. Thanks
Roger, The <repeat> construct creates an array of the various inputs over which you can iterate within the command template of your tool config. See the concatenate datasets wrapper (tools/filters/catWrapper.xml) for a full example, but here are the relevant sections inline: <repeat name="queries" title="Dataset"> <param name="input2" type="data" label="Select" /> </repeat> <command interpreter="python"> catWrapper.py $out_file1 $input1 #for $q in $queries ${q.input2} #end for </command> -Dannon On Dec 13, 2011, at 9:47 PM, Roger Ngo wrote:
Hello all,
I have a question on how the <repeat> tag works in a Galaxy tool XML file.
Right now I have a perl script that takes in various arguments. One of the arguments I have is a repeated one which is just a file selection feature.
The script works something like this:
script.pl $arg1 $arg2 $varyingNumOfArgs
By using <repeat>, is the execution of the script something like this?
script.pl $arg1 $arg2 $repeatedArg1 $repeatedArg2 ... $repeatedArgN
where repeatedArgs1 ... repeatedArgsN are basically arguments specified by the <repeat> tag.
If so, is there a certain way to access these repeated arguments and pass them into my script in the <command> tag? This is the part where I am not quite sure how <repeat> works.
Thanks ___________________________________________________________ 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:
Thanks Dannon! This was exactly what I was looking for! On Tue, Dec 13, 2011 at 7:29 PM, Dannon Baker <dannonbaker@me.com> wrote:
Roger,
The <repeat> construct creates an array of the various inputs over which you can iterate within the command template of your tool config. See the concatenate datasets wrapper (tools/filters/catWrapper.xml) for a full example, but here are the relevant sections inline:
<repeat name="queries" title="Dataset"> <param name="input2" type="data" label="Select" /> </repeat>
<command interpreter="python"> catWrapper.py $out_file1 $input1 #for $q in $queries ${q.input2} #end for </command>
-Dannon
On Dec 13, 2011, at 9:47 PM, Roger Ngo wrote:
Hello all,
I have a question on how the <repeat> tag works in a Galaxy tool XML file.
Right now I have a perl script that takes in various arguments. One of the arguments I have is a repeated one which is just a file selection feature.
The script works something like this:
script.pl $arg1 $arg2 $varyingNumOfArgs
By using <repeat>, is the execution of the script something like this?
script.pl $arg1 $arg2 $repeatedArg1 $repeatedArg2 ... $repeatedArgN
where repeatedArgs1 ... repeatedArgsN are basically arguments specified by the <repeat> tag.
If so, is there a certain way to access these repeated arguments and pass them into my script in the <command> tag? This is the part where I am not quite sure how <repeat> works.
Thanks ___________________________________________________________ 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:
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Dannon Baker -
Roger Ngo