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author refinery-platform
date Thu, 22 Feb 2018 14:14:03 -0500
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1 <?xml version='1.0' encoding='utf-8'?>
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3 <tool id="refinery_test_N-1" name="Refinery test tool N-1" version="0.1">
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4 <description>for testing Galaxy workflow execution from Refinery</description>
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5 <command>
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6 <![CDATA[
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7 ## Argparse expects many values for a single arg to be in the form of: -i INUPT INPUT1 INPUT2 ...
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8 #set $inputs = " ".join([$input_file.__str__ for $input_file in $input_col])
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9
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10 ## Run the test tool with the N inputs from our Dataset Collection
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11 $__tool_directory__/refinery_test_tool.py -i $inputs -o $output_file -e $exit_code -p $p_fail -s $sleep_time $stdout $stderr $empty_outfile
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param name="input_col" type="data_collection" collection_type="list" label="Input file"/>
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16 <param name="sleep_time" type="integer" label="Sleep (seconds)" value="0" min="0"/>
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17 <param name="empty_outfile" type="boolean" label="Produce empty output file" truevalue="--empty_outfile" falsevalue=""/>
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18 <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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19 <param name="stdout" type="boolean" label="Write to standard out" truevalue="--stdout" falsevalue=""/>
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20 <param name="stderr" type="boolean" label="Write to standard error" truevalue="--stderr" falsevalue=""/>
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21 <param name="exit_code" type="integer" label="Exit code [0, 255]" value="0" min="0" max="255"/>
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22 </inputs>
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23 <outputs>
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24 <data format="txt" name="output_file" label="Refinery Test Tool N-1 Output" />
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25 </outputs>
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26 <stdio>
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27 <exit_code range="1:" level="fatal" />
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28 <regex match=".+" source="stdout" level="fatal" description="Tool produced output to standard out" />
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29 <regex match=".+" source="stderr" level="fatal" description="Tool produced output to standard error" />
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30 </stdio>
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31 <tests>
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32 <test>
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33 <param name="input_col">
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34 <collection type="list">
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35 <element name="1" value="file1.txt"/>
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36 <element name="2" value="file2.txt"/>
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37 <element name="3" value="file3.txt"/>
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38 </collection>
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39 </param>
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40 <param name="sleep_time" type="integer" label="Sleep (seconds)" value="0" min="0"/>
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41 <param name="empty_outfile" type="boolean" label="Produce empty output file" truevalue="--empty_outfile" falsevalue=""/>
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42 <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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43 <param name="stdout" type="boolean" label="Write to standard out" truevalue="--stdout" falsevalue=""/>
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44 <param name="stderr" type="boolean" label="Write to standard error" truevalue="--stderr" falsevalue=""/>
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45 <param name="exit_code" type="integer" label="Exit code [0, 255]" value="0" min="0" max="255"/>
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46 <output name="output_file">
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47 <assert_contents>
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48 <has_text text="Contents of File 1" />
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49 <has_text text="Contents of File 2" />
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50 <has_text text="Contents of File 3" />
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51 </assert_contents>
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52 </output>
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53 </test>
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54 </tests>
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55 <help>
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56 .. class:: infomark
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57
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58 **Purpose**
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59
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60 To test Galaxy workflow execution and monitoring from Refinery.
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61
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62 -----
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63
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64 .. class:: infomark
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65
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66 **Inputs and outputs**
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67
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68 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.
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69
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70 *Note:* You must set the "Probability of failure" parameter to a non-zero value
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71 for "Write to standard out", "Write to standard error" or "Exit code" to take effect.
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72 </help>
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73 </tool>