--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/axttomaf.xml	Tue Aug 27 07:33:54 2024 +0000
@@ -0,0 +1,105 @@
+<tool id="ucsc_axtomaf" name="axtToMaf" version="@TOOL_VERSION@+galaxy0" profile="21.05" license="MIT">
+    <description>
+        Convert dataset from axt to MAF 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-axttomaf</requirement>
+    </requirements>
+    <version_command><![CDATA[ echo "@TOOL_VERSION@" ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+    axtToMaf
+        '$in_axt'
+        #if str( $target_reference_index_source.target_reference_index_source_selector ) == "history":
+            '${target_reference_index_source.in_tar_ref_index}'
+        #else:
+            '$target_reference_index_source.tar_ref_index_file.fields.path'
+        #end if
+        #if str( $query_reference_index_source.query_reference_index_source_selector ) == "history":
+            '${query_reference_index_source.in_que_ref_index}'
+        #else:
+            '$query_reference_index_source.que_ref_index_file.fields.path'
+        #end if
+        '$out'
+    ]]></command>
+    <inputs>
+        <param name="in_axt" format="axt" type="data" label="axt file" />
+
+        <conditional name="target_reference_index_source">
+            <param name="target_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
+                <option value="cached">Built-in</option>
+                <option value="history">My history</option>
+            </param>
+            <when value="cached">
+                <param name="tar_ref_index_file" type="select" label="Using reference genome index">
+                  <options from_data_table="fasta_indexes" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="in_tar_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for target sequence. Typically a '.fai' file." />
+            </when>
+        </conditional>
+
+        <conditional name="query_reference_index_source">
+            <param name="query_reference_index_source_selector" type="select" label="Choose the source for the target reference genome index">
+                <option value="cached">Built-in</option>
+                <option value="history">My history</option>
+            </param>
+            <when value="cached">
+                <param name="que_ref_index_file" type="select" label="Using reference genome index">
+                  <options from_data_table="fasta_indexes" />
+                </param>
+            </when>
+            <when value="history">
+                <param name="in_que_ref_index" format="tabular" type="data" label="Dataset with chrom sizes for query sequence. Typically a '.fai' file." />
+            </when>
+        </conditional>
+
+    </inputs>
+    <outputs>
+        <data name="out" format="maf" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="in_axt" value="1.axt"/>
+            <conditional name="target_reference_index_source">
+                <param name="target_reference_index_source_selector" value="history" />
+                <param name="in_tar_ref_index" value="hg38.fasta.fai"/>
+            </conditional>
+            <conditional name="query_reference_index_source">
+                <param name="query_reference_index_source_selector" value="history" />
+                <param name="in_que_ref_index" value="mm39.fasta.fai"/>
+            </conditional>
+            <output name="out" file="1.maf"/>
+        </test>
+        <test>
+            <param name="in_axt" value="1.axt"/>
+            <conditional name="target_reference_index_source">
+                <param name="target_reference_index_source_selector" value="cached" />
+                <param name="tar_ref_index_file" value="hg38"/>
+            </conditional>
+            <conditional name="query_reference_index_source">
+                <param name="query_reference_index_source_selector" value="cached" />
+                <param name="que_ref_index_file" value="mm39"/>
+            </conditional>
+            <output name="out" file="1.maf"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+`axtToMaf`_ is a tool to convert dataset from `axt format`_ to `MAF format`_.
+
+.. _axtToMaf: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/FOOTER.txt
+.. _axt format: https://genome.ucsc.edu/goldenPath/help/axt.html
+.. _MAF format: https://genome.ucsc.edu/FAQ/FAQformat.html#format5
+    ]]>    </help>
+    <citations>
+        <citation type="doi">10.1093/bib/bbs038</citation>
+    </citations>
+</tool>