galaxy/tools/expression_tools/parse_values_from_file.xml

<tool name="Parse parameter value" id="param_value_from_file" version="0.1.0" tool_type="expression" profile="19.05">
    <description>from dataset</description>
    <macros>
        <import>expression_macros.xml</import>
    </macros>
    <expression type="ecma5.1">{
var output;
if ($job.remove_newlines || $job.param_type != 'text') {
   $job.input1.contents = $job.input1.contents.trim();
}
if ($job.param_type == 'integer') {
    output = parseInt($job.input1.contents);
} else if ($job.param_type == 'float') {
    output = parseFloat($job.input1.contents);
} else if ($job.param_type == 'boolean') {
    const trueValues = ['yes', 'true', '1']
    const falseValues = ['no', 'false', '0']
    let lowerCaseContents = $job.input1.contents.toLowerCase();
    if (trueValues.includes(lowerCaseContents)) {
        output = true;
    } else if (falseValues.includes(lowerCaseContents)) {
        output = false;
    }
    else {
        return 'NOT A BOOLEAN VALUE';
    }
} else {
    output = $job.input1.contents;
}
return {'output': output};
    }</expression>
    <inputs>
        <param type="data" label="Input file containing parameter to parse out of" load_contents="64000" name="input1" />
        <param name="param_type" type="select" label="Select type of parameter to parse">
            <option value="text">Text</option>
            <option value="integer">Integer</option>
            <option value="float">Float</option>
            <option value="boolean">Boolean</option>
        </param>
        <param name="remove_newlines" checked="true" type="boolean" label="Remove newlines ?" help="Uncheck this only if newlines should be preserved in parameter"/>
    </inputs>
    <expand macro="typed_outputs" />
    <tests>
        <test expect_num_outputs="1">
            <param name="input1" value="simple_line.txt"/>
            <param name="param_type" value="text"/>
            <param name="remove_newlines" value="true"/>
            <output name="text_param">
                <assert_contents>
                    <has_line line="&quot;This is a line of text.&quot;"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input1" value="simple_line.txt"/>
            <param name="param_type" value="text"/>
            <param name="remove_newlines" value="false"/>
            <output name="text_param">
                <assert_contents>
                    <has_line line="&quot;This is a line of text.\n&quot;"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input1" value="1.integer.txt"/>
            <param name="param_type" value="integer"/>
            <param name="remove_newlines" value="false"/>
            <output name="integer_param">
                <assert_contents>
                    <has_line line="1"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input1" value="1.integer.txt"/>
            <param name="param_type" value="float"/>
            <param name="remove_newlines" value="false"/>
            <output name="float_param">
                <assert_contents>
                    <has_line line="1"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input1" value="1.bool.txt"/>
            <param name="param_type" value="boolean"/>
            <param name="remove_newlines" value="false"/>
            <output name="boolean_param">
                <assert_contents>
                    <has_line line="false"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help></help>
</tool>