diff netchainsubset.xml @ 0:6d5ab8d81db2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset commit 203061071dae562277de62b43680fc9bae853f35

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/netchainsubset.xml	Wed Jan 14 09:16:58 2026 +0000
@@ -0,0 +1,58 @@
+<tool id="ucsc_netchainsubset" name="netChainSubset" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        Create chain file with subset of chains that appear in the net
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">482</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">ucsc-netchainsubset</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    netChainSubset
+        '$in_net'
+        '$in_chain'
+        '$out'
+        $splitOnInsert
+        $wholeChains
+        $skipMissing
+    ]]></command>
+    <inputs>
+        <param name="in_net" format="ucsc.net" type="data" label="net dataset" help="" />
+        <param name="in_chain" format="chain" type="data" label="chain dataset" help="" />
+        <param argument="-splitOnInsert" type="boolean" optional="true" truevalue="-splitOnInsert" falsevalue="" label="Split on insert" help="Split chain when get an insertion of another chain." />
+        <param argument="-wholeChains" type="boolean" optional="true" truevalue="-wholeChains" falsevalue="" label="Whole chains" help="Write entire chain references by net, don't split when a high-level net is encoundered.  This is useful when nets have been filtered." />
+        <param argument="-skipMissing" type="boolean" optional="true" truevalue="-skipMissing" falsevalue="" label="Skip missing chains" help="Skip chains that are not found instead of generating an error. Useful if chains have been filtered." />
+    </inputs>
+    <outputs>
+        <data name="out" format="chain" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="in_net" value="target.net" />
+            <param name="in_chain" value="in.chain" />
+            <output name="out" file="out.chain" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`netChainSubset`_ is a tool to create a `chain`_ file with subset of chains that appear in the net.
+This process creates so called `liftOver`_ file used to convert coordinates between asesemblies.
+
+For implementation details see netChainSubset's `source code`_.
+
+.. _netChainSubset: https://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER
+.. _net: https://genome.ucsc.edu/goldenPath/help/net.html
+.. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
+.. _liftOver: https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Liftover
+.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/151a59e4e7526124ff096019c6c4052f0a900711/src/hg/mouseStuff/netChainSubset/netChainSubset.c
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
+    </citations>
+</tool>