Re: [galaxy-dev] Conditionally showing certain form elements on tool page
On 08/15/2012 08:59 PM, Dan Tenenbaum wrote: Hi all, I'm trying to wrap my head around what the conditional tag does...it looks like it doesn't do what I would like. I want to create a tool that allows the user to upload a data file and then have it run through one or more filters. Each filter takes one or more parameters. I was thinking I could do something like this: inputs conditional name=mycond param name=checktest type=boolean label=foo value=yessir /param when value=yessir param name=param1 type=text label=bar value=twunk /param /when /conditional /inputs The idea being, if the user checks the box labeled foo, a text box labeled bar will appear. And I would have several such checkboxes and their accompanying parameters. But what I get is just the checkbox, and nothing happens when I click it. Is it possible to do what I have in mind, and if so, how? Also note that these conditions are not mutually exclusive. A user can select one *or more* filters. So I'm not sure how the body of my command tag should look. Is there a way I can just pass every possible parameter to my script like this: myscript.py param1=foo param2=bar If a parameter is not defined (because the user didn't click its associated checkbox), then the script will receive e.g. param1= param2=bar but it can deal with that. I realize I can make several tools and chain them together in a workflow, but that seems like overkill for this use case, and it would be nice if the user could set up their desired filters on one screen. Is this possible? Thanks! Dan ___ 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/ Hello Dan, The easiest way to go about this, since you said that none of your filters are mutually exclusive, is to use the select datatype. I don't think you even need the conditional tags. Galaxy says that you need when tag sets when you use conditionals, but this is not true, as I have similar code as I have written below. Use type=select in your parameter. This gives you a button that can have a multitude of options, but most of mine are simply used like booleans. Something like this: inputs param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param param name=param2 type=select label=filter2Name help=more helpful tips option value=yesyes/option option value=nono/option /param /inputs I had certain options that WERE mutually exclusive, and required nested conditional statements, where I had an outer conditional for the extra options, and an inner conditional around each parameter. As for the command tag, the select type parameters make it easy because you can just check the string values with an if statement, like so: (assuming python) command interpreter=python tool.py #if $param1 == yes: --YourGetOptFlag #else: ##dont even need an else, just ignore #end if /command If I am not mistaken, this should be sufficient if all you need to pass is a flag indicating your program to use the filter. If you need to pass a flag AND integer values, you are going to have to wrap your parameters in conditional tags and use a set of when: inputs conditional name=firstConditional param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param when value=yes param name=IntegerBox type=integer value=[default value] min=(optional) max=(optional) label=UseParamName help=helpful text / /when when value=no / !--Doesnt show integer text box when no is chosen in the select-- /conditional /inputs Rinse and repeat, adding conditionals around each select. I think this is actually what you want to do, as you say you want a box to appear after a user selects whether or not to use the filter. Also, quick note, the text between the option tags are what appear on the select buttons, so they can be whatever you want. The value= is the important thing, as this is what you will evaluate the if/else to in the command tag. One last thing, The cheetah command is really no different. command interpreter=python tool.py #if $firstConditional.param1 == yes: --testGetOpt $firstConditional.IntegerBox #end if /command The second command tag is how I pass a few parameters into my command line tool. Anyway, I hope this helped a little bit. If you need anything else, let me know and I will see If I can help. A lot of this was trial and error and I am sure there are trickier ways to doing it, but this worked for the scope of my program. -John
Re: [galaxy-dev] Conditionally showing certain form elements on tool page
Hi John, On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote: On 08/15/2012 08:59 PM, Dan Tenenbaum wrote: Hi all, I'm trying to wrap my head around what the conditional tag does...it looks like it doesn't do what I would like. I want to create a tool that allows the user to upload a data file and then have it run through one or more filters. Each filter takes one or more parameters. I was thinking I could do something like this: inputs conditional name=mycond param name=checktest type=boolean label=foo value=yessir /param when value=yessir param name=param1 type=text label=bar value=twunk /param /when /conditional /inputs The idea being, if the user checks the box labeled foo, a text box labeled bar will appear. And I would have several such checkboxes and their accompanying parameters. But what I get is just the checkbox, and nothing happens when I click it. Is it possible to do what I have in mind, and if so, how? Also note that these conditions are not mutually exclusive. A user can select one *or more* filters. So I'm not sure how the body of my command tag should look. Is there a way I can just pass every possible parameter to my script like this: myscript.py param1=foo param2=bar If a parameter is not defined (because the user didn't click its associated checkbox), then the script will receive e.g. param1= param2=bar but it can deal with that. I realize I can make several tools and chain them together in a workflow, but that seems like overkill for this use case, and it would be nice if the user could set up their desired filters on one screen. Is this possible? Thanks! Dan ___ 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/ Hello Dan, The easiest way to go about this, since you said that none of your filters are mutually exclusive, is to use the select datatype. I don't think you even need the conditional tags. Galaxy says that you need when tag sets when you use conditionals, but this is not true, as I have similar code as I have written below. Use type=select in your parameter. This gives you a button that can have a multitude of options, but most of mine are simply used like booleans. Something like this: inputs param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param param name=param2 type=select label=filter2Name help=more helpful tips option value=yesyes/option option value=nono/option /param /inputs I had certain options that WERE mutually exclusive, and required nested conditional statements, where I had an outer conditional for the extra options, and an inner conditional around each parameter. As for the command tag, the select type parameters make it easy because you can just check the string values with an if statement, like so: (assuming python) command interpreter=python tool.py #if $param1 == yes: --YourGetOptFlag #else: ##dont even need an else, just ignore #end if /command If I am not mistaken, this should be sufficient if all you need to pass is a flag indicating your program to use the filter. If you need to pass a flag AND integer values, you are going to have to wrap your parameters in conditional tags and use a set of when: inputs conditional name=firstConditional param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param when value=yes param name=IntegerBox type=integer value=[default value] min=(optional) max=(optional) label=UseParamName help=helpful text / /when when value=no / !--Doesnt show integer text box when no is chosen in the select-- /conditional /inputs Rinse and repeat, adding conditionals around each select. I think this is actually what you want to do, as you say you want a box to appear after a user selects whether or not to use the filter. Also, quick note, the text between the option tags are what appear on the select buttons, so they can be whatever you want. The value= is the important thing, as this is what you will evaluate the if/else to in the command tag. One last thing, The cheetah command is really no different. command interpreter=python tool.py #if $firstConditional.param1 == yes: --testGetOpt $firstConditional.IntegerBox #end if /command The second command tag is how I pass a few parameters into my command line tool. Anyway, I hope this helped a little bit. If you need anything else, let me know and I will see If I can help. A
Re: [galaxy-dev] Conditionally showing certain form elements on tool page
On Thu, Aug 16, 2012 at 10:53 AM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi John, On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote: On 08/15/2012 08:59 PM, Dan Tenenbaum wrote: Hi all, I'm trying to wrap my head around what the conditional tag does...it looks like it doesn't do what I would like. I want to create a tool that allows the user to upload a data file and then have it run through one or more filters. Each filter takes one or more parameters. I was thinking I could do something like this: inputs conditional name=mycond param name=checktest type=boolean label=foo value=yessir /param when value=yessir param name=param1 type=text label=bar value=twunk /param /when /conditional /inputs The idea being, if the user checks the box labeled foo, a text box labeled bar will appear. And I would have several such checkboxes and their accompanying parameters. But what I get is just the checkbox, and nothing happens when I click it. Is it possible to do what I have in mind, and if so, how? Also note that these conditions are not mutually exclusive. A user can select one *or more* filters. So I'm not sure how the body of my command tag should look. Is there a way I can just pass every possible parameter to my script like this: myscript.py param1=foo param2=bar If a parameter is not defined (because the user didn't click its associated checkbox), then the script will receive e.g. param1= param2=bar but it can deal with that. I realize I can make several tools and chain them together in a workflow, but that seems like overkill for this use case, and it would be nice if the user could set up their desired filters on one screen. Is this possible? Thanks! Dan ___ 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/ Hello Dan, The easiest way to go about this, since you said that none of your filters are mutually exclusive, is to use the select datatype. I don't think you even need the conditional tags. Galaxy says that you need when tag sets when you use conditionals, but this is not true, as I have similar code as I have written below. Use type=select in your parameter. This gives you a button that can have a multitude of options, but most of mine are simply used like booleans. Something like this: inputs param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param param name=param2 type=select label=filter2Name help=more helpful tips option value=yesyes/option option value=nono/option /param /inputs I had certain options that WERE mutually exclusive, and required nested conditional statements, where I had an outer conditional for the extra options, and an inner conditional around each parameter. As for the command tag, the select type parameters make it easy because you can just check the string values with an if statement, like so: (assuming python) command interpreter=python tool.py #if $param1 == yes: --YourGetOptFlag #else: ##dont even need an else, just ignore #end if /command If I am not mistaken, this should be sufficient if all you need to pass is a flag indicating your program to use the filter. If you need to pass a flag AND integer values, you are going to have to wrap your parameters in conditional tags and use a set of when: inputs conditional name=firstConditional param name=param1 type=select label=filterName help=helpful tips option value=yesyes/option option value=nono/option /param when value=yes param name=IntegerBox type=integer value=[default value] min=(optional) max=(optional) label=UseParamName help=helpful text / /when when value=no / !--Doesnt show integer text box when no is chosen in the select-- /conditional /inputs Rinse and repeat, adding conditionals around each select. I think this is actually what you want to do, as you say you want a box to appear after a user selects whether or not to use the filter. Also, quick note, the text between the option tags are what appear on the select buttons, so they can be whatever you want. The value= is the important thing, as this is what you will evaluate the if/else to in the command tag. One last thing, The cheetah command is really no different. command interpreter=python tool.py #if $firstConditional.param1 == yes: --testGetOpt $firstConditional.IntegerBox #end if /command The second command tag is how I pass a few parameters into my command line tool. Anyway, I hope this helped a little
Re: [galaxy-dev] Conditionally showing certain form elements on tool page
On Thu, Aug 16, 2012 at 6:53 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi John, On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote: Hello Dan, The easiest way to go about this, since you said that none of your filters are mutually exclusive, is to use the select datatype. I don't think you even need the conditional tags. Galaxy says that you need when tag sets when you use conditionals, but this is not true, as I have similar code as I have written below. Use type=select in your parameter. This gives you a button that can have a multitude of options, but most of mine are simply used like booleans. Something like this: ... This is extremely helpful! Thanks. I find the select box yes/no idiom a bit awkward. I'd prefer a checkbox (just a single one, not one each for yes and no) but doing a select box is ok too, I can live with that. Using a boolean checkbox should work - although early on it wasn't possible thus many older tools use a select instead: https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-boolean-with-conditional 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] Conditionally showing certain form elements on tool page
Hi John and Peter, On Thu, Aug 16, 2012 at 11:37 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Aug 16, 2012 at 6:53 PM, Dan Tenenbaum dtene...@fhcrc.org wrote: Hi John, On Thu, Aug 16, 2012 at 9:51 AM, John Patterson jmpa...@g.uky.edu wrote: Hello Dan, The easiest way to go about this, since you said that none of your filters are mutually exclusive, is to use the select datatype. I don't think you even need the conditional tags. Galaxy says that you need when tag sets when you use conditionals, but this is not true, as I have similar code as I have written below. Use type=select in your parameter. This gives you a button that can have a multitude of options, but most of mine are simply used like booleans. Something like this: ... This is extremely helpful! Thanks. I find the select box yes/no idiom a bit awkward. I'd prefer a checkbox (just a single one, not one each for yes and no) but doing a select box is ok too, I can live with that. Using a boolean checkbox should work - although early on it wasn't possible thus many older tools use a select instead: https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-boolean-with-conditional I can do a checkbox like this: param name=cbtest type=boolean label=checkbox help=some help/ But I want to have a checkbox that triggers some other params to appear when it is checked (the way I have successfully done it with a select). I haven't been able to figure that out. If I do this: conditional name=thirdConditional param name=param2 type=boolean value=yes label=Filter 3 help=helpful tips / when value=yes param name=IntegerBox3 type=integer value=1 min=0 max=5 label=A parameter to filter 3 help=helpful text / /when when value=no / /conditional ...nothing happens when I click the checkbox. I also tried using a select with multiple=true and display=checkbox, but Galaxy doesn't like that because I provide only one option (yes). If you could tell me how to cause params to appear/disappear by checking a checkbox that would be great! Thanks, Dan 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] Conditionally showing certain form elements on tool page
On 08/15/2012 08:59 PM, Dan Tenenbaum wrote: Hi all, I'm trying to wrap my head around what the conditional tag does...it looks like it doesn't do what I would like. I want to create a tool that allows the user to upload a data file and then have it run through one or more filters. Each filter takes one or more parameters. I was thinking I could do something like this: inputs conditional name=mycond param name=checktest type=boolean label=foo value=yessir /param when value=yessir param name=param1 type=text label=bar value=twunk /param /when /conditional /inputs The idea being, if the user checks the box labeled foo, a text box labeled bar will appear. And I would have several such checkboxes and their accompanying parameters. But what I get is just the checkbox, and nothing happens when I click it. Is it possible to do what I have in mind, and if so, how? Also note that these conditions are not mutually exclusive. A user can select one *or more* filters. So I'm not sure how the body of my command tag should look. Is there a way I can just pass every possible parameter to my script like this: myscript.py param1=foo param2=bar If a parameter is not defined (because the user didn't click its associated checkbox), then the script will receive e.g. param1= param2=bar but it can deal with that. I realize I can make several tools and chain them together in a workflow, but that seems like overkill for this use case, and it would be nice if the user could set up their desired filters on one screen. Is this possible? Thanks! Dan ___ 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/ Hello Dan, This page really helped me understand how the tags worked as well as looking at some older tools: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax I will take a look at my tool when I get to the office tomorrow. John ___ 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/
