--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/axtchain.xml	Mon Aug 26 17:34:17 2024 +0000
@@ -0,0 +1,92 @@
+<tool id="ucsc_axtchain" name="axtChain" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        Chain together axt alignments
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">455</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">ucsc-axtchain</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    axtChain
+        -faQ
+        -faT
+        #if $minScore
+            -minScore='$minScore'
+        #end if
+        #if $scoreScheme
+            -scoreScheme='$scoreScheme'
+        #end if
+        #if str($linear_gap_options.linear_gap) == "linear_gap_file"
+            -linearGap='${linear_gap_options.lineargap_input}'
+        #else
+            -linearGap=$linear_gap_options.linear_gap
+        #end if
+        '$in_axt'
+        '$in_target'
+        '$in_query'
+        '$out'
+    ]]></command>
+    <inputs>
+        <param name="in_axt" format="axt" type="data" label="Alignments" />
+        <param name="in_target" format="fasta" type="data" label="Target sequence" help="Make sure you are using the same name in both alignment and source sequence e.g. hg38.chr1"/>
+        <param name="in_query" format="fasta" type="data" label="Query sequence" help="Make sure you are using the same name in both alignment and source sequence e.g. mm39.chr1"/>
+
+        <conditional name="linear_gap_options">
+            <param label="Specify type of linear gap costs to use" name="linear_gap" type="select">
+                <option selected="true" value="loose">loose (chicken/human linear gap costs)</option>
+                <option value="medium">medium (mouse/human linear gap costs)</option>
+                <option value="linear_gap_file">Provide a dataset with linear gap costs</option>
+            </param>
+            <when value="medium" />
+            <when value="loose" />
+            <when value="linear_gap_file">
+                <param name="lineargap_input" type="data" format="tabular" label="Read the linear gap costs from" help="See help for a sample file"/>
+            </when>
+        </conditional>
+
+        <param argument="-minScore" type="integer" optional="true" label="Minimum score for chain" help="Default 1000" />
+        <param argument="-scoreScheme" type="data" format="tabular" optional="true" label="Read the scoring matrix from a blastz-format file" />
+    </inputs>
+    <outputs>
+        <data name="out" format="chain" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_axt" value="hg38.chrM.mm39.chrM.axt" />
+            <param name="in_target" value="hg38.chrM.fasta" />
+            <param name="in_query" value="mm39.chrM.fasta" />
+            <conditional name="linear_gap_options">
+                <param name="linear_gap" value="medium" />
+            </conditional>
+            <output name="out" file="hg38.chrM.mm39.chrM.chain" />
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`axtChain`_ is a tool to chain together alignments. The `chain`_ format describes a pairwise alignment that allow gaps in both sequences simultaneously.
+
+
+sample linearGap file (loose)::
+
+    tablesize       11
+    smallSize       111
+    position        1       2       3       11      111     2111    12111   32111   72111   152111  252111
+    qGap    325     360     400     450     600     1100    3600    7600    15600   31600   56600
+    tGap    325     360     400     450     600     1100    3600    7600    15600   31600   56600
+    bothGap 625     660     700     750     900     1400    4000    8000    16000   32000   57000
+
+
+.. _axtChain: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+.. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
+    </citations>
+</tool>