--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maftoaxt.xml	Wed Jul 31 14:29:06 2024 +0000
@@ -0,0 +1,72 @@
+<tool id="maftoaxt" name="mafToAxt" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        Convert file from MAF to axt format
+    </description>
+    <macros>
+        <token name="@TOOL_VERSION@">377</token>
+    </macros>
+    <xrefs>
+        <xref type="bio.tools">UCSC_Genome_Browser_Utilities</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">ucsc-maftoaxt</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        mafToAxt
+            '$in_maf'
+            #if $tar_seq.tarSeq == "customTar"
+                '$tar_seq.targetSeq'
+            #else
+                first
+            #end if
+            '$querySeq'
+            '$out'
+            $stripDb
+        ]]></command>
+        <inputs>
+            <param name="in_maf" format="maf" type="data" label="maf file" />
+
+            <conditional name="tar_seq">
+                <param name="tarSeq" type="select" label="Select target sequence" optional="false" help="Which sequence from the MAF file should be used as the target sequence. ">
+                    <option value="" selected="true">Use the first sequence of the block as the target</option>
+                    <option value="customTar">Specify the target sequence by name</option>
+                </param>
+                <when value="customTar">
+                    <param optional="false" name="targetSeq" type="text" label="Name of sequence that should be used as target sequence" help="Must be present in the MAF file." />
+                </when>
+                <when value="" />
+            </conditional>
+
+            <param name="querySeq" type="text" optional="false" label="Name of sequence that should be used as the query sequence" help="Must be present in the MAF file." />
+            <param argument="-stripDb" type="boolean" truevalue="-stripDb" falsevalue="" label="Strip names from start to the first period" help="'hg38.chr19' becomes 'chr19'" />
+
+        </inputs>
+        <outputs>
+            <data name="out" format="axt" />
+        </outputs>
+        <tests>
+            <test>
+                <param name="in_maf" value="1.maf"/>
+                <param name="querySeq" value="panTro1"/>
+                <output name="out" file="1.axt"/>
+            </test>
+            <test>
+                <param name="in_maf" value="1.maf"/>
+                <param name="tarSeq" value="customTar"/>
+                <param name="targetSeq" value="panTro1"/>
+                <param name="querySeq" value="rn3"/>
+                <output name="out" file="2.axt"/>
+            </test>
+        </tests>
+        <help><![CDATA[
+    **What it does**
+
+    `mafToAxt`_ is a tool to convert maf dataset to axt format. Depending on parameters and the number of alignments in the MAF file this can be a full conversion or data extraction.
+
+    .. _mafToAxt: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+        ]]>    </help>
+        <citations>
+            <citation type="doi">10.1093/bib/bbs038</citation>
+        </citations>
+    </tool>