--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mafFrag.xml	Tue Sep 09 16:20:32 2025 +0000
@@ -0,0 +1,82 @@
+<tool id="ucsc_maffrag" name="mafFrag" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+    <description>Extract MAF sequences for a region from database</description>
+    <macros>
+        <token name="@TOOL_VERSION@">482</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@PROFILE@">24.2</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">ucsc-maffrag</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+        <![CDATA[
+        cp '$ucsc_db_connection' "\${HOME}/.hg.conf" &&
+        chmod 600 "\${HOME}/.hg.conf" &&
+        mafFrag '$genome' '$track' '$chrom' '$start' '$end' '$strand' out.maf
+        ]]>
+    </command>
+    <configfiles>
+        <configfile name="ucsc_db_connection"><![CDATA[
+#European MariaDB server
+db.host=genome-euro-mysql.soe.ucsc.edu
+db.user=genomep
+db.password=password
+central.db=hgcentral
+central.host=genome-euro-mysql.soe.ucsc.edu
+central.user=genomep
+central.password=password
+gbdbLoc1=http://hgdownload.soe.ucsc.edu/gbdb/
+forceTwoBit=on 
+        ]]></configfile>
+    </configfiles>
+    <inputs>
+        <param name="genome" type="text" optional="false" label="Enter Genome database name" help="Name should match with the UCSC Table Browser Entries (For Eg. mm10, hg19, hg38)"/>
+        <param name="track" type="text" optional="false" label="Enter UCSC Table name for desired table of the above genome" help="Table name should match with the UCSC Table Browser Entries (For eg. knownGene, all_mrna)"/>
+        <param name="chrom" type="text" optional="false" label="Chromosome" help="Chromosome name (e.g., chr1, chr2, etc.)"/>
+        <param name="start" type="integer" optional="false" label="Start position" help="Start position of the region in the chromosome (0-based)"/>
+        <param name="end" type="integer" optional="false" label="End position" help="End position of the region in the chromosome (0-based)"/>
+        <param name="strand" type="select" optional="false" label="Strand" help="Strand of the region">
+            <option value=".">No Strand</option>
+            <option value="+">Forward Strand(+)</option>
+            <option value="-">Reverse Strand(-)</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="maf" from_work_dir="out.maf" label="${tool.name} on ${on_string}:Output MAF"/>
+    </outputs>
+    <tests>
+        <!-- Test 01: Testing with default options -->
+        <test expect_num_outputs="1">
+            <param name="genome" value="hg19"/>
+            <param name="track" value="multiz46way"/>
+            <param name="chrom" value="chr17"/>
+            <param name="start" value="7578370"/>
+            <param name="end" value="7578400"/>
+            <param name="strand" value="+"/>
+            <output name="output" ftype="maf">
+                <assert_contents>
+                    <has_n_lines n="43"/>
+                    <has_size value="3087"/>
+                    <has_line line="s hg19.chr17 7578370 30 + 81195210 CA---TCGCTA----TCTGAG--CAGCGCTC-ATGGTGGG"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+mafFrag is a command-line tool from the UCSC Genome Browser suite that extracts MAF sequences for a region from database.
+
+    ]]></help>
+        <citations>
+            <citation type="bibtex">
+                @misc{mafFrag,
+                author = {Kent UCSC},
+                title = {mafFrag: A tool that extracts MAF sequences for a region from database},
+                note = {Tool that extracts MAF sequences for a region from database}
+            </citation>
+    </citations>
+    <creator>
+        <person givenName="Saim" familyName="Momin" url="https://github.com/SaimMomin12" identifier="https://orcid.org/0009-0003-9935-828X"/>
+        <organization name="Galaxy Europe" url="https://galaxyproject.org/eu/"/>
+    </creator>
+</tool>
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