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comparison planemotest/planemotest.xml @ 1:0183cad9d13b draft

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planemo upload
author fubar
date Thu, 22 Feb 2024 10:48:01 +0000
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0:2beaae16651e 1:0183cad9d13b
1 <tool name="planemotest" id="planemotest" version="0.01">
2 <!--Source in git at: https://github.com/fubar2/galaxy-->
3 <!--Created by toolfactory@galaxy.org at 25/05/2023 01:04:53 using the Galaxy Tool Factory.-->
4 <description>Tests a ToolFactory archive containing a new tool</description>
5 <requirements>
6 <requirement version="0.75.18" type="package">planemo</requirement>
7 </requirements>
8 <stdio>
9 <exit_code range="1:" level="fatal"/>
10 </stdio>
11 <version_command><![CDATA[echo "0.01"]]></version_command>
12 <command><![CDATA[bash
13 $runme
14 $Toolshed_archive_to_be_tested
15 $test_output]]></command>
16 <configfiles>
17 <configfile name="runme"><![CDATA[#raw
18
19 ### script for ToolFactory toolshed archive test tool
20 mkdir testout
21 tar -xvf $1
22 TOOLNAME=`find . -name "*.xml"`
23 FIXED=$(basename "$TOOLNAME" | cut -d. -f1)
24 REP=testout/"$FIXED"_planemo_test_report.html
25 planemo test --update_test_data --test_output $REP $TOOLNAME > STDOUT
26 cp $REP $2
27
28 #end raw]]></configfile>
29 </configfiles>
30 <inputs>
31 <param name="Toolshed_archive_to_be_tested" type="data" optional="false" label="Toolshed archive to be tested" help="" format="tgz" multiple="false"/>
32 </inputs>
33 <outputs>
34 <data name="test_output" format="html" label="test_output" hidden="false"/>
35 </outputs>
36 <tests>
37 <test>
38 <output name="test_output" value="test_output_sample" compare="diff" lines_diff="5"/>
39 <param name="Toolshed_archive_to_be_tested" value="Toolshed_archive_to_be_tested_sample"/>
40 </test>
41 </tests>
42 <help><![CDATA[
43
44 **What it Does**
45
46 Tests a tool archive with Planemo
47
48 Runs planemo test and returns a toolshed archive updated with test outputs and a Planemo test result.
49
50 NOTE: First run takes 5+ minutes as Planemo is installed by Conda.
51 The second and subsequent runs don't have that startup time.
52
53 Dogfood demonstration - this tool was generated with the ToolFactory and is included as a sample of what's possible and potentially useful.
54
55 ------
56
57
58 Script::
59
60 ### script for ToolFactory toolshed archive test tool
61 mkdir testout
62 tar -xvf $1
63 TOOLNAME=`find . -name "*.xml"`
64 FIXED=$(basename "$TOOLNAME" | cut -d. -f1)
65 LOG=testout/"$FIXED"_planemo_test_log.txt
66 REP=testout/"$FIXED"_planemo_test_report.html
67 echo "using $LOG and $REP"
68 echo "## Found toolname = $TOOLNAME" > $LOG
69 planemo test --update_test_data --test_output $REP $TOOLNAME >> $LOG
70 cp $REP $2
71
72 ]]></help>
73 <citations>
74 <citation type="doi">10.1093/bioinformatics/bts573</citation>
75 </citations>
76 </tool>
77