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

planemo upload
author fubar
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
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+<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>
+