galaxy/test/functional/tools/detect_errors.xml

<tool id="detect_errors" name="detect_errors" version="1.0.0">
    <stdio>
       <exit_code range="3:5" level="warning" description="Low disk space" />
       <exit_code range="6:"  level="fatal"   description="Bad input dataset" />
       <exit_code range="2"   level="fatal_oom"   description="Out of Memory" />
       <regex match="message" source="stdout" level="log" description="some program message of interest"/>
       <regex match="low space" source="both" level="warning" description="Low space on device" />
       <regex match="error" source="stderr" level="fatal" description="Unknown error encountered" />
       <regex match="out of memory" source="stdout" level="fatal_oom" description="Out of memory error occurred" />
       <regex match="[CG]{12}" description="Fatal error - CG island 12 nts long found" />
       <regex match="^Branch A" level="warning" description="Branch A was taken in execution" />
    </stdio>
    <command><![CDATA[
#if str($stdoutmsg) != ""
    echo '$stdoutmsg' &&
#end if
#if str($stderrmsg) != ""
    >2& echo '$stderrmsg' && 
#end if
sh -c 'exit $exit_code'
    ]]>
    </command>
    <inputs>
        <param name="stdoutmsg" type="text" value="" label="messages to stdout" />
        <param name="stderrmsg" type="text" value="" label="messages to stderr" />
        <param name="exit_code" type="integer" value="0" label="exit code"/>
    </inputs>
    <outputs>
        <data name="out_file1" />
    </outputs>
    <tests>
        <!-- exit code + regex tests -->
        <!-- successful run (warning exit code + log and warning messages) -->
        <test expect_exit_code="3" expect_failure="false">
            <param name="stdoutmsg" value="message: everything is fine" />
            <param name="stderrmsg" value="low space" />
            <param name="exit_code" value="3" />
            <assert_stdout>
                <has_line line="Log: some program message of interest"/>
                <has_line line="Warning: Low space on device"/>
            </assert_stdout>
            <assert_stderr>
                <has_line line="Warning: Exit code 3 (Low disk space)"/>
            </assert_stderr>
        </test>
        <!-- unccessful run (fatal exit code + warning in output messages are detected) -->
        <test expect_exit_code="23" expect_failure="true">
            <param name="stdoutmsg" value="Branch A seems to be of iterest .. maybe its related to the error?" />
            <param name="exit_code" value="23" />
            <assert_stdout>
                <has_line line="Warning: Branch A was taken in execution"/>
            </assert_stdout>
            <assert_stderr>
                <has_line line="Fatal error: Exit code 23 (Bad input dataset)"/>
            </assert_stderr>
        </test>
        <!-- unccessful run (fatal exit code + fatal_oom message is detected) -->
        <test expect_exit_code="6" expect_failure="true">
            <param name="stdoutmsg" value="out of memory" />
            <param name="exit_code" value="6" />
            <assert_stdout>
                <has_line line="Out of memory error: Out of memory error occurred"/>
            </assert_stdout>
            <assert_stderr>
                <has_line line="Fatal error: Exit code 6 (Bad input dataset)"/>
            </assert_stderr>
        </test>
        <!-- unccessful run (good exit code + fatal message) -->
        <test expect_exit_code="0" expect_failure="true">
            <param name="stdoutmsg" value="CGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCGCG" />
            <param name="exit_code" value="0" />
            <assert_stdout>
                <has_line line="Fatal error: Fatal error - CG island 12 nts long found"/>
            </assert_stdout>
        </test>
        <!-- unccessful run (fatal oom exit code + fatal_oom message is detected .. latter is expected to be undetected) -->
        <test expect_exit_code="2" expect_failure="true">
            <param name="stdoutmsg" value="out of memory" />
            <param name="exit_code" value="2" />
            <assert_stdout>
                <not_has_text text="Out of memory error: Out of memory error occurred"/>
                <has_line line="out of memory"/>
            </assert_stdout>
            <assert_stderr>
                <has_line line="Out of memory error: Exit code 2 (Out of Memory)"/>
            </assert_stderr>
        </test>

        <!-- exit code tests -->
        <!-- successful run -->
        <test expect_exit_code="0" expect_failure="false">
            <param name="stdoutmsg" value="everything is fine" />
            <param name="exit_code" value="0" />
            <assert_stdout>
                <has_line line="everything is fine"/>
            </assert_stdout>
        </test>
        <!-- exit code without meaning -->
        <test expect_exit_code="1" expect_failure="false">
            <param name="stdoutmsg" value="everything is fine" />
            <param name="exit_code" value="1" />
            <assert_stdout>
                <has_line line="everything is fine" />
            </assert_stdout>
        </test>
        <!-- exit code indicating warning -->
        <test expect_exit_code="4" expect_failure="false">
            <param name="stdoutmsg" value="everything is fine" />
            <param name="exit_code" value="4" />
            <assert_stdout>
                <has_line line="everything is fine" />
            </assert_stdout>
        </test>
        <!-- exit code indicating error -->
        <test expect_exit_code="42" expect_failure="true">
            <param name="stdoutmsg" value="everything just seems fine so far... but it isn't" />
            <param name="exit_code" value="42" />
            <assert_stdout>
                <has_line line="everything just seems fine so far... but it isn__sq__t" />
            </assert_stdout>
            <assert_stderr>
                <has_line line="Fatal error: Exit code 42 (Bad input dataset)" />
            </assert_stderr>
        </test>
        <!-- exit code indicating oom_error -->
        <test expect_exit_code="2" expect_failure="true">
            <param name="stdoutmsg" value="everything just seems fine so far... but it isn't" />
            <param name="exit_code" value="2" />
            <assert_stdout>
                <has_line line="everything just seems fine so far... but it isn__sq__t" />
            </assert_stdout>
            <assert_stderr>
                <has_line line="Out of memory error: Exit code 2 (Out of Memory)" />
            </assert_stderr>
        </test>
    </tests>
    <help>
    </help>
</tool>