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Simple Parameters

We have built a tool wrapper for the seqtk seq command - but this tool actually has additional options that we may wish to expose the Galaxy user.

Lets take a few of the parameters from the help command and build Galaxy param blocks to stick in the tool's inputs block.

-V        shift quality by '(-Q) - 33'

In the previous section we saw param block of type data for input files, but there are many different kinds of parameters one can use. Flag parameters such as the above -V parameter are frequently represented by boolean parameters in Galaxy tool XML.

<param name="shift_quality" type="boolean" label="Shift quality"
       truevalue="-V" falsevalue=""
       help="shift quality by '(-Q) - 33' (-V)" />

We can then stick $shift_quality in our command block and if the user has selected this option it will be expanded as -V (since we have defined this as the truevalue). If the user hasn't selected this option $shift_quality will just expand as an empty string and not affect the generated command line.

Now consider the following seqtk seq parameters:

-q INT    mask bases with quality lower than INT [0]
-X INT    mask bases with quality higher than INT [255]

These can be translated into Galaxy parameters as:

<param name="quality_min" type="integer" label="Mask bases with quality lower than"
       value="0" min="0" max="255" help="(-q)" />
<param name="quality_max" type="integer" label="Mask bases with quality higher than"
       value="255" min="0" max="255" help="(-X)" />

These can be add to the command tag as -q $quality_min -X $quality_max.

At this point the tool would look like:

.. literalinclude:: writing/seqtk_seq_v4.xml
   :language: xml
   :emphasize-lines: 7-10,14-20

Conditional Parameters

The previous parameters were simple because they always appeared, now consider.

-M FILE   mask regions in BED or name list FILE [null]

We can mark this data type param as optional by adding the attribute optional="true".

<param name="mask_regions" type="data" label="Mask regions in BED"
       format="bed" help="(-M)" optional="true" />

Then instead of just using $mask_regions directly in the command block, one can wrap it in an if statement (because tool XML files support Cheetah).

#if $mask_regions
-M '$mask_regions'
#end if

Next consider the parameters:

-s INT    random seed (effective with -f) [11]
-f FLOAT  sample FLOAT fraction of sequences [1]

In this case, the -s random seed parameter should only be seen or used if the sample parameter is set. We can express this using a conditional block.

<conditional name="sample">
    <param name="sample_selector" type="boolean" label="Sample fraction of sequences" />
    <when value="true">
        <param name="fraction" label="Fraction" type="float" value="1.0"
               help="(-f)" />
        <param name="seed" label="Random seed" type="integer" value="11"
               help="(-s)" />
    </when>
    <when value="false">
    </when>
</conditional>

In our command block, we can again use an if statement to include these parameters.

#if $sample.sample_selector
-f $sample.fraction -s $sample.seed
#end if

Notice we must reference the parameters using the sample. prefix since they are defined within the sample conditional block.

The newest version of this tool is now

.. literalinclude:: writing/seqtk_seq_v5.xml
   :language: xml
   :emphasize-lines: 10-16,28-40

For tools like this where there are many options but in the most uses the defaults are preferred - a common idiom is to break the parameters into simple and advanced sections using a conditional.

Updating this tool to use that idiom might look as follows.

.. literalinclude:: writing/seqtk_seq_v6.xml
   :language: xml
   :emphasize-lines: 7-18,23-30,51-52