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