Hi everyone,
I started to use the option from_data_table in xml file instead of from_file as it is recommended by galaxy. It works well when I write the name defined in the tool_data_table, for example :
xml file :
<param name="species" type="select" label="Select species for ID conversion" >
<options from_data_table="id_mapping_file"/>
</param>
tool_data_table :
<tables>
<table name="id_mapping_file" comment_char="#">
<columns>value, name, path</columns>
<file path="tool-data/id_mapping_file.loc" />
</table>
</tables>
id_mapping_file.loc :
human_id_mapping Human (homo sapiens) [path]/human_id_mapping_file.tsv
mouse_id_mapping Mouse (Mus musculus) [path]/mouse_id_mapping.tsv
I have a dropdown menu with two choices : Human (homo sapiens) and Mouse (Mus musculus).
But when I try to use the value from the loc file in a conditional, the value appears as not defined, for example :
xml_file :
<conditional name="species">
<param name="mapping_file" type="select" label="Select species for ID conversion" >
<options from_data_table="id_mapping_file"/>
</param>
<when value="human_id_mapping">
something...
</when>
<when value="mouse_id_mapping">
something...
</when>
</conditional>
It is not working and I get the following error with planemo lint :
.. WARNING: No <option /> found for when block 'human_id_mapping' inside conditional 'species'
.. WARNING: No <option /> found for when block 'mouse_id_mapping' inside conditional 'species'
Does anyone knows how to use values from a loc file in conditional statement ? I can only use it in the command section ($species.mapping_file).