Hi, I have created a tool that will fetch sequences for selected IDs from a tabular file containing multiple IDs and additional info.

I want the tool config to scan the first column of the tab file for IDs and provide the user with a selection box where they can select a single ID or multiple IDs and get output for all selected.

The following method does this:

<param name="tabfile" type="data" format="tabular" label="ID File"/>
<param name="selection" type="select" multiple="true" accept_default="true" label="ID" >
              <options from_dataset="tabfile">
                              <column name="name" index="0"/>
                              <column name="value" index="0"/>

The issue is, if the top file in my history is a SAM file containing ~30,000 IDs in the first column the tool initially attempts to load these all in to the selection box and effectively crashes my local instance.

I only want to use this on tab files that ill have ~100 IDs at most. I have got around this by creating a new datatype indexfile as a class of Tabular in tabular.py:

class IndexFile( Tabular ):
    file_ext = 'indexfile'

    def sniff( self, filename ):
        return False

And changing the input file to:
<param name="tabfile" type="data" format="tabular" label="ID File"/>

This means I must first set the tabular file to type indexfile, then it will be the only dataset shown under tabfile.

Selecting options from a file is really useful, I was wondering if there is a better workaround for this or if a similar indexfile datatype could be included in Galaxy.


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