Mercurial > repos > fubar > mashmap
diff planemotest/planemotest.xml @ 1:0183cad9d13b draft
planemo upload
author | fubar |
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date | Thu, 22 Feb 2024 10:48:01 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemotest/planemotest.xml Thu Feb 22 10:48:01 2024 +0000 @@ -0,0 +1,77 @@ +<tool name="planemotest" id="planemotest" version="0.01"> + <!--Source in git at: https://github.com/fubar2/galaxy--> + <!--Created by toolfactory@galaxy.org at 25/05/2023 01:04:53 using the Galaxy Tool Factory.--> + <description>Tests a ToolFactory archive containing a new tool</description> + <requirements> + <requirement version="0.75.18" type="package">planemo</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + <version_command><![CDATA[echo "0.01"]]></version_command> + <command><![CDATA[bash +$runme +$Toolshed_archive_to_be_tested +$test_output]]></command> + <configfiles> + <configfile name="runme"><![CDATA[#raw + +### script for ToolFactory toolshed archive test tool +mkdir testout +tar -xvf $1 +TOOLNAME=`find . -name "*.xml"` +FIXED=$(basename "$TOOLNAME" | cut -d. -f1) +REP=testout/"$FIXED"_planemo_test_report.html +planemo test --update_test_data --test_output $REP $TOOLNAME > STDOUT +cp $REP $2 + +#end raw]]></configfile> + </configfiles> + <inputs> + <param name="Toolshed_archive_to_be_tested" type="data" optional="false" label="Toolshed archive to be tested" help="" format="tgz" multiple="false"/> + </inputs> + <outputs> + <data name="test_output" format="html" label="test_output" hidden="false"/> + </outputs> + <tests> + <test> + <output name="test_output" value="test_output_sample" compare="diff" lines_diff="5"/> + <param name="Toolshed_archive_to_be_tested" value="Toolshed_archive_to_be_tested_sample"/> + </test> + </tests> + <help><![CDATA[ + +**What it Does** + +Tests a tool archive with Planemo + +Runs planemo test and returns a toolshed archive updated with test outputs and a Planemo test result. + +NOTE: First run takes 5+ minutes as Planemo is installed by Conda. +The second and subsequent runs don't have that startup time. + +Dogfood demonstration - this tool was generated with the ToolFactory and is included as a sample of what's possible and potentially useful. + +------ + + +Script:: + + ### script for ToolFactory toolshed archive test tool + mkdir testout + tar -xvf $1 + TOOLNAME=`find . -name "*.xml"` + FIXED=$(basename "$TOOLNAME" | cut -d. -f1) + LOG=testout/"$FIXED"_planemo_test_log.txt + REP=testout/"$FIXED"_planemo_test_report.html + echo "using $LOG and $REP" + echo "## Found toolname = $TOOLNAME" > $LOG + planemo test --update_test_data --test_output $REP $TOOLNAME >> $LOG + cp $REP $2 + +]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/bts573</citation> + </citations> +</tool> +