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3
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1 <tool id="refinery_test_2-2" name="Refinery test tool 2-2" version="0.1">
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2 <description>for testing Galaxy workflow execution from Refinery</description>
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3
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4 <command interpreter="python">
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8
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5 refinery_test_tool.py -i $input_file1 $input_file2 -o $output_file1 $output_file2 -e $exit_code -p $p_fail -s $sleep_time $stdout $stderr $empty_outfile
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3
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6 </command>
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7
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8 <inputs>
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9 <param name="input_file1" format="txt" type="data" label="Input file A"/>
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10 <param name="input_file2" format="txt" type="data" label="Input file B"/>
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11 <param name="sleep_time" type="integer" label="Sleep (seconds)" value="0" min="0"/>
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8
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12 <param name="empty_outfile" type="boolean" label="Produce empty output files" truevalue="--empty_outfile" falsevalue=""/>
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3
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13 <param name="p_fail" type="float" label="Probability of failure [0.0, 1.0]" value="0.0" min="0.0" max="1.0"/>
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14 <param name="stdout" type="boolean" label="Write to standard out" truevalue="--stdout" falsevalue=""/>
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15 <param name="stderr" type="boolean" label="Write to standard error" truevalue="--stderr" falsevalue=""/>
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16 <param name="exit_code" type="integer" label="Exit code [0, 255]" value="0" min="0" max="255"/>
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17 </inputs>
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18
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19 <outputs>
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20 <data format="txt" name="output_file1" label="Output file A"/>
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21 <data format="txt" name="output_file2" label="Output file B"/>
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22 </outputs>
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23
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24 <stdio>
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25 <exit_code range="1:" level="fatal" />
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26 <regex match=".+" source="stdout" level="fatal" description="Tool produced output to standard out" />
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27 <regex match=".+" source="stderr" level="fatal" description="Tool produced output to standard error" />
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28 </stdio>
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29
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30 <help>
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31
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32 .. class:: infomark
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33
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34 **Purpose**
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35
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36 To test Galaxy workflow execution and monitoring from Refinery.
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37
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38 -----
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39
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40 .. class:: infomark
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41
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42 **Inputs and outputs**
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43
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4
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44 This wrapper will accept two text files as input and produce two output files
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45 with concatenated content from input files.
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46
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47 *Note:* You must set the "Probability of failure" parameter to a non-zero value
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48 for "Write to standard out", "Write to standard error" or "Exit code" to take effect.
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49
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50 </help>
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51 </tool>
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