view refinery_test_2-6.xml @ 6:66d49d9635b1 draft

Add sample five step workflow.

<tool id="refinery_test_2-6" name="Refinery test tool 2-6" version="0.1">
    <description>for testing Galaxy workflow execution from Refinery</description>

    <command interpreter="python">
        refinery_test_tool.py -i $input_file1 $input_file2 -o $output_file1 $output_file2 $output_file3 $output_file4 $output_file5 $output_file6 -e $exit_code -p $p_fail -s $sleep_time $stdout $stderr
    </command>

    <inputs>
        <param name="input_file1" format="txt" type="data" label="Input file A"/>
        <param name="input_file2" format="txt" type="data" label="Input file B"/>
        <param name="sleep_time" type="integer" label="Sleep (seconds)" value="0" min="0"/>
        <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_file1" label="Output file A"/>
        <data format="txt" name="output_file2" label="Output file B"/>
        <data format="txt" name="output_file3" label="Output file C"/>
        <data format="txt" name="output_file4" label="Output file D"/>
        <data format="txt" name="output_file5" label="Output file E"/>
        <data format="txt" name="output_file6" label="Output file F"/>
    </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>

    <help>

.. class:: infomark

**Purpose**

To test Galaxy workflow execution and monitoring from Refinery.

-----

.. class:: infomark

**Inputs and outputs**

This wrapper will accept two text files as input and produce six output files
with concatenated content from input files.

*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>