--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nettoaxt.xml	Thu Sep 19 17:13:14 2024 +0000
@@ -0,0 +1,66 @@
+<tool id="ucsc_nettoaxt" name="netToAxt" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        Convert net (and chain) to axt format
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">469</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">ucsc-nettoaxt</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    netToAxt
+        '$in_net'
+        '$in_chain'
+        '$in_target'
+        '$in_query'
+        '$out'
+        $qChain
+        #if str($maxGap)
+            -maxGap=$maxGap
+        #end if
+        $noSplit
+    ]]></command>
+    <inputs>
+        <param name="in_net" format="ucsc.net" type="data" label="Net dataset" />
+        <param name="in_chain" format="chain" type="data" label="Chain dataset" />
+        <param name="in_target" format="twobit" type="data" label="Dataset with target sequence" />
+        <param name="in_query" format="twobit" type="data" label="Dataset with query sequence" />
+        <param argument="-qChain" type="boolean" optional="true" truevalue="-qChain" falsevalue="" label="Is the net with respect to the query side of chains?" />
+        <param argument="-maxGap" type="integer" optional="true" min="0" label="Maximum size of gap before breaking" help="default 100" />
+        <param argument="-noSplit" type="boolean" optional="true" truevalue="-noSplit" falsevalue="" label="Don't split chain when there is an insertion of another chain" />
+
+    </inputs>
+    <outputs>
+        <data name="out" format="axt" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_net" value="hg38.chrM.mm39.chrM.ucsc.net" />
+            <param name="in_chain" value="hg38.chrM.mm39.chrM.chain" />
+            <param name="in_target" value="hg38.chrM.twobit" />
+            <param name="in_query" value="mm39.chrM.twobit" />
+            <output name="out" file="out.axt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`netToAxt`_ is a tool from the UCSC suite to convert dataset from `ucsc.net`_ format (and `alignment chains`_) to `axt`_ format.
+
+For implementation details see netToAxt's `source code`_.
+
+.. _netToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+.. _ucsc.net: https://genome.ucsc.edu/goldenPath/help/net.html
+.. _alignment chains: https://genome.ucsc.edu/goldenPath/help/chain.html
+.. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
+.. _source code: https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/mouseStuff/netToAxt/netToAxt.c
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
+    </citations>
+</tool>
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