comparison refinery_test_N-1.xml @ 1:b87749d7a24c draft default tip

planemo upload commit 4fb0a789956149e5a58f4e370d7fe14f4e8bcf79

1:b87749d7a24c

<?xml version='1.0' encoding='utf-8'?>

<tool id="refinery_test_N-1" name="Refinery test tool N-1" version="0.1">
    <description>for testing Galaxy workflow execution from Refinery</description>
    <command>
        <![CDATA[
            ## Argparse expects many values for a single arg to be in the form of: -i INUPT INPUT1 INPUT2 ...
            #set $inputs = " ".join([$input_file.__str__ for $input_file in $input_col])

            ## Run the test tool with the N inputs from our Dataset Collection
            $__tool_directory__/refinery_test_tool.py -i $inputs -o $output_file -e $exit_code -p $p_fail -s $sleep_time $stdout $stderr $empty_outfile
        ]]>
    </command>
    <inputs>
        <param name="input_col" type="data_collection" collection_type="list" label="Input file"/>
        <param name="sleep_time" type="integer" label="Sleep (seconds)" value="0" min="0"/>
        <param name="empty_outfile" type="boolean" label="Produce empty output file" truevalue="--empty_outfile" falsevalue=""/>
        <param name="p_fail" type="float" label="Probability of failure [0.0, 1.0]" value="0.0" min="0.0" max="1.0"/>
        <param name="stdout" type="boolean" label="Write to standard out" truevalue="--stdout" falsevalue=""/>
        <param name="stderr" type="boolean" label="Write to standard error" truevalue="--stderr" falsevalue=""/>
        <param name="exit_code" type="integer" label="Exit code [0, 255]" value="0" min="0" max="255"/>
    </inputs>
    <outputs>
        <data format="txt" name="output_file" label="Refinery Test Tool N-1 Output" />
    </outputs>
    <stdio>
        <exit_code range="1:" level="fatal" />
        <regex match=".+" source="stdout" level="fatal" description="Tool produced output to standard out" />
        <regex match=".+" source="stderr" level="fatal" description="Tool produced output to standard error" />
    </stdio>
	<tests>
  		<test>
			<param name="input_col">
            	<collection type="list">
                	<element name="1" value="file1.txt"/>
                	<element name="2" value="file2.txt"/>
                	<element name="3" value="file3.txt"/>
            	</collection>
        	</param>
			<param name="sleep_time" type="integer" label="Sleep (seconds)" value="0" min="0"/>
        	<param name="empty_outfile" type="boolean" label="Produce empty output file" truevalue="--empty_outfile" falsevalue=""/>
        	<param name="p_fail" type="float" label="Probability of failure [0.0, 1.0]" value="0.0" min="0.0" max="1.0"/>
        	<param name="stdout" type="boolean" label="Write to standard out" truevalue="--stdout" falsevalue=""/>
        	<param name="stderr" type="boolean" label="Write to standard error" truevalue="--stderr" falsevalue=""/>
        	<param name="exit_code" type="integer" label="Exit code [0, 255]" value="0" min="0" max="255"/>
    		<output name="output_file">
				<assert_contents>
            		<has_text text="Contents of File 1" />
					<has_text text="Contents of File 2" />
					<has_text text="Contents of File 3" />
        		</assert_contents>
			</output>		
		</test>
	</tests>
    <help>
        .. class:: infomark

        **Purpose**

        To test Galaxy workflow execution and monitoring from Refinery.

        -----

        .. class:: infomark

        **Inputs and outputs**

        This wrapper will accept A Dataset collection list as input and produce a single output file with the concatenated, annotated content of each element in the Dataset Collection.

        *Note:* You must set the "Probability of failure" parameter to a non-zero value
        for "Write to standard out", "Write to standard error" or "Exit code" to take effect.
    </help>
</tool>