--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abslen_bed/abslen_bed.xml	Thu Feb 22 10:48:01 2024 +0000
@@ -0,0 +1,56 @@
+<tool name="abslen_bed" id="abslen_bed" version="1" profile="22.05">
+  <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
+  <!--Created by toolfactory@galaxy.org at 10/12/2023 11:37:03 using the Galaxy Tool Factory.-->
+  <description>Returns a file of absolute values from differences</description>
+  <requirements>
+    <requirement type="package">python</requirement>
+  </requirements>
+  <version_command><![CDATA[echo "1"]]></version_command>
+  <command><![CDATA[python
+'$runme'
+<
+$absin
+>
+$absout]]></command>
+  <configfiles>
+    <configfile name="runme"><![CDATA[#raw
+import sys
+inp = []
+for line in sys.stdin:
+    if line.strip() > '':
+        ls = line.split()
+        if len(ls) > 2:
+            x = abs(int(ls[2]) - int(ls[1]))
+            ls.append((str(x)))
+            inp.append('\t'.join(ls))
+    else:
+        break
+sys.stdout.write('\n'.join(inp))
+#end raw]]></configfile>
+  </configfiles>
+  <inputs>
+    <param name="absin" type="data" optional="false" label="absin" help="Input file to be converted using abs()" format="csfasta,txt,tabular" multiple="false"/>
+  </inputs>
+  <outputs>
+    <data name="absout" format="bed" hidden="false"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="absin" value="absin_sample"/>
+      <output name="absout" value="absout_sample"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+ **What it Does**
+ Takes absolute values on the input 
+ 
+ This tool is a temporary step to enable the Sanger TreeVal NF gap_finder workflow to be
+ translated into Galaxy
+ 
+ See https://github.com/fubar2/treeval_gal/tree/main/gap_finder
+  ]]></help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/bts573</citation>
+  </citations>
+</tool>
+