Some parameters of IQ-TREE such as --date-tip and --date-ci are not passed into the command line

[jerryakii]

UseGalaxy.ca user reported some parameters such as --date-tip and --date-ci were not passed into the command line when using IQ-Tree. Based on the XML (https://github.com/galaxyproject/tools-iuc/blob/main/tools/iqtree/iqtree.xml), these parameters seem to not be included:

## date options
#if str($time_tree.date_source.select_source) == 'dataset':
    #if $time_tree.date_source.date:
        --date '$time_tree.date_source.date'
    #end if
#elif str($time_tree.date_source.select_source) == 'input':
    --date TAXNAME
    #if str($time_tree.date_source.date_tip) != '':
        --date-tip '$time_tree.date_source.date_tip'
    #end if
    #if str($time_tree.date_source.date_root) != '':
        --date-root '$time_tree.date_source.date_root'
    #end if
    #if str($time_tree.date_source.date_ci) != '':
        --date-ci '$time_tree.date_source.date_ci'
    #end if
    #if str($time_tree.date_source.clock_sd) != '':
        --clock-sd '$time_tree.date_source.clock_sd'
    #end if
    #if str($time_tree.date_source.date_outlier) != '':
        --date-outlier '$time_tree.date_source.date_outlier'
    #end if
    #if str($time_tree.date_source.date_options) != '':
        --date-options '$time_tree.date_source.date_options'
    #end if
    --dating LSD
    $time_tree.date_source.date_no_outgroup
#end if

[lsterck]

Hi,

can you add some info/context here?
given the code: they are included when non-empty and "input" as source eg.:

#elif str($time_tree.date_source.select_source) == 'input':
    --date TAXNAME
    #if str($time_tree.date_source.date_tip) != '':
        --date-tip '$time_tree.date_source.date_tip'
    #end if

I'm not super familiar with IQ-Tree myself so I might miss out on the nitty-gritty here.

[jerryakii]

For sure. When using IQ-Tree, and expand "Time Tree Reconstruction", there are two options for "Source of Date Information": "Text file" or "Derive from input". Our users in useGalaxy.ca found that when selecting "Text file", those parameters such as "--date-tip", "--date-ci" were not passed into the command for running. Please correct me if I am wrong. Based on the xml file, #if str($time_tree.date_source.select_source) == 'dataset': means selecting "Text file" while #elif str($time_tree.date_source.select_source) == 'input': means selecting "Derive from input". So if the user select "Text file", it seems those parameters won't be passed into the commands?

Thanks!
Jerry

[wm75]

Isn't the idea of the text file that the file should provide the information? Then the issue would be that the wrapper misleadingly still displays the functionless input fields. I'm not sure though of what can be part of the text file.