[galaxy-dev] Filtering number of outputs with a conditional
Hello Galaxians, I am currently working on a tool to format reports but I have a problem with the filter tag. A little example is easier to figure than a long explanation so... My xml looks like this: tool name=My tool id=my tool command interpreter=python$SCRIPTTYPE.SCRIPT $REPORT $SECONDPARAM $OUTFILE $MAP/command inputs param type=data label=My input file name=REPORT help=Just for the example/ conditional name=SCRIPTTYPE param type=select label=Script to use name=SCRIPT option value=script_x.pyX/option option value=script_y.pyY/option option value=script_z.pyZ/option /param when value=script_x.py param type=select name=SECONDPARAM label=My parameter option value=foofoo/option option value=barbar/option /param /when when value=script_y.py param type=select name=SECONDPARAM label=My parameter option value=AA/option option value=BB/option /param /when when value=script_z.py param type=select name=SECONDPARAM label=My parameter option value=11/option option value=22/option /param /when /conditional /inputs outputs data type=data format=tabular name=OUTFILE label=My outfile filter SCRIPTTYPE['SCRIPT'] == script_x.py/filter /data data type=data name=OUTFILE label=My_outfile.tgz filter SCRIPTTYPE['SCRIPT'] == script_y.py/filter /data data type=data format=tabular name=OUTFILE label=My other outfile filter SCRIPTTYPE['SCRIPT'] == script_z.py/filter /data data type=data format=tabular name=MAPFILE label=My map filter SCRIPTTYPE['SCRIPT'] == script_z.py/filter /data /outputs /tool = I try to make my xml work that way: When I select my script x, there is only one output labeled my outfile. When I select my script y, there is only one output labeled My_outfile.tgz When I select my script z, there are two outputs. I had it working properly with just x or y, but when I add z to my xml, the thing gets all buggy. Instead of having one output when I select x or y, I always have two outputs my other outfile and my map as if I had selected z. Do you have any idea how I could solve that? Thank you, best regards, Alexandre ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Filtering number of outputs with a conditional
On Thu, Oct 31, 2013 at 10:41 AM, Alexandre Loywick a.loyw...@gmail.com wrote: Hello Galaxians, I am currently working on a tool to format reports but I have a problem with the filter tag. A little example is easier to figure than a long explanation so... My xml looks like this: ... Do you have any idea how I could solve that? Personally, I would probably have three separate XML files, one for each script. Since they are doing different jobs and producing different sets of output that seems much clearer (and will make life easier in the workflow editor too later on). If there is a lot of commonality you can use macros in the XML to avoid repeating things like input parameters. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Filtering number of outputs with a conditional
Thank you for your fast answer Peter, The thing is I have some constraints about this developpement and creating multiple tools for similar processes is a bit annoying so... I'm not really aware of macros in the xml, I'll go read the wiki again about that. bests, Alexandre 2013/10/31 Peter Cock p.j.a.c...@googlemail.com On Thu, Oct 31, 2013 at 10:41 AM, Alexandre Loywick a.loyw...@gmail.com wrote: Hello Galaxians, I am currently working on a tool to format reports but I have a problem with the filter tag. A little example is easier to figure than a long explanation so... My xml looks like this: ... Do you have any idea how I could solve that? Personally, I would probably have three separate XML files, one for each script. Since they are doing different jobs and producing different sets of output that seems much clearer (and will make life easier in the workflow editor too later on). If there is a lot of commonality you can use macros in the XML to avoid repeating things like input parameters. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Filtering number of outputs with a conditional
On Thu, Oct 31, 2013 at 11:02 AM, Alexandre Loywick a.loyw...@gmail.com wrote: Thank you for your fast answer Peter, The thing is I have some constraints about this developpement and creating multiple tools for similar processes is a bit annoying so... I'm not really aware of macros in the xml, I'll go read the wiki again about that. bests, Alexandre In addition to the wiki documentation, for a complex set of examples Bjoern and John have used the macros to remove a LOT of duplication in the BLAST+ XML files, https://github.com/peterjc/galaxy_blast/tree/master/tools/ncbi_blast_plus The repeated snippets are defined here: https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_macros.xml Note there are two kinds, XML and tokens - the tokens are new and not yet on the wiki. They can be used inside the Cheetah syntax for the command tag and also the RST markup for the help tag. In a simple case (and the older BLAST+ versions) we'd just reference the macros file from the individual tools with: macros importncbi_macros.xml/import /macros You insert the XML macros with lines like this: expand macro=input_conditional_choose_db_type / This is fairly easy (although it can be harder to debug). 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
