Dummy Galaxy tool demonstrating problem with setting value of boolean parameter used as "control" variable in a conditional tag within tool tests

galaxy_boolean_test_issue2.sh

#!/bin/sh
echo Values are ${@:2} > $1

galaxy_boolean_test_issue2.xml

<tool id="boolean_issue2" name="Boolean test issue 2" version="1.1">
<description>Demonstrate issue with using booleans in Galaxy tests</description>
<command interpreter="bash">
  galaxy_boolean_test_issue2.sh
  $output_1 $bdg1 $bdg_options.bdg2
  #if str($bdg_options.bdg2) == 'True'
     -B2 $bdg_options.spmr
     #if str($bdg_options.make_bigwig) == 'True'
         --make-big-wig
     #end if
  #end if
</command>
<inputs>
  <!-- Normal boolean -->
  <param name="bdg1" type="boolean" checked="False"
	 truevalue="-B1" falsevalue="" label="Save pileups in bedGraph?" />
  <!-- Boolean used for conditional -->
  <conditional name="bdg_options">
    <param name="bdg2" type="boolean" checked="False"
	   truevalue="-B2" falsevalue="" label="Save pileups in bedGraph?" />
    <when value="-B2">
      <param name="spmr" type="boolean" checked="False"
	     truevalue="--SPMR" falsevalue="" label="Use --SPMR?" />
      <param name="make_bigwig" type="boolean" checked="True"
	     truevalue="True" falsevalue="" label="Generate bigWig?" />
    </when>
    <when value="">
      <!-- Display nothing -->
    </when>
  </conditional>
</inputs>
<outputs>
  <data name="output_1" format="txt" label="Values of booleans" />
</outputs>
<tests>
  <test>
    <!-- #0: don't set any params explicitly -->
    <output name="output_1">
      <assert_contents>
	<has_line line="Values are False" />
      </assert_contents>
    </output>
  </test>
  <test>
    <!-- #1: set non-conditional boolean only to true -->
    <param name="bdg1" value="true" />
    <output name="output_1">
      <assert_contents>
	<has_line line="Values are -B1 False" />
      </assert_contents>
    </output>
  </test>
  <test>
    <!-- #2: (try to) set conditional boolean to true using 'bdg2' -->
    <param name="bdg1" value="true" />
    <param name="bdg2" value="true" />
    <output name="output_1">
      <assert_contents>
	<has_line line="Values are -B1 True -B2 --make-big-wig" />
      </assert_contents>
    </output>
  </test>
  <test>
    <!-- #3: (try to) set conditional boolean to true using 'bdg_options|bdg2'-->
    <param name="bdg1" value="true" />
    <param name="bdg_options|bdg2" value="true" />
    <output name="output_1">
      <assert_contents>
	<has_line line="Values are -B1 True -B2 --make-big-wig" />
      </assert_contents>
    </output>
  </test>
  <test>
    <!-- #4: (try to) set conditional boolean to true using 'bdg_options.bdg2' -->
    <param name="bdg1" value="true" />
    <param name="bdg_options.bdg2" value="true" />
    <output name="output_1">
      <assert_contents>
	<has_line line="Values are -B1 True -B2 --make-big-wig" />
      </assert_contents>
    </output>
  </test>
  <test>
    <!-- #5: (try to) set conditional boolean to -B2 using 'bdg2' -->
    <param name="bdg1" value="true" />
    <param name="bdg2" value="-B2" />
    <output name="output_1">
      <assert_contents>
	<has_line line="Values are -B1 True -B2 --make-big-wig" />
      </assert_contents>
    </output>
  </test>
  <test>
    <!-- #6: (try to) set conditional boolean to -B2 using 'bdg_options|bdg2'-->
    <param name="bdg1" value="true" />
    <param name="bdg_options|bdg2" value="-B2" />
    <output name="output_1">
      <assert_contents>
	<has_line line="Values are -B1 True -B2 --make-big-wig" />
      </assert_contents>
    </output>
  </test>
  <test>
    <!-- #7: (try to) set conditional boolean to -B2 using 'bdg_options.bdg2' -->
    <param name="bdg1" value="true" />
    <param name="bdg_options.bdg2" value="-B2" />
    <output name="output_1">
      <assert_contents>
	<has_line line="Values are -B1 True -B2 --make-big-wig" />
      </assert_contents>
    </output>
  </test>
</tests>
</tool>