--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/embl2fa.xml	Sun Nov 13 00:23:23 2022 +0000
@@ -0,0 +1,35 @@
+<tool id="embl2fa" name="Convert embl flat file to fasta" version="0.1">
+  <description></description>
+  <stdio>
+      <exit_code range="1:" level="fatal" description="Tool exception" />
+  </stdio>
+  <command detect_errors="exit_code"><![CDATA[
+       grep -P "(^ID)|(^ +[GATCNgatcn ]+\d+)" "$input" > "$output" &&
+       sed -i -E "s/^ID   />/" "$output" &&
+       sed -i -E "s/(>[^ ]+) .+/\1/g"  "$output" &&
+       sed -i -E "s/([GATCNgatcn]+) /\1/g" "$output" &&
+       sed -i -E "s/^ +//g" "$output" &&
+       sed -i -E "s/ +[0-9]+//g" "$output"
+  ]]></command>
+  <inputs>
+      <param format="txt" name="input" type="data" label="EMBL flat file" />
+  </inputs>
+  <outputs>
+    <data name="output" format="fasta" label="fasta file" />
+  </outputs>
+  <tests>
+      <test>
+          <param name="input" value="transposon_sequence_set_v9.5.embl.txt" ftype="txt" />
+          <output name="output" file="transposon_sequence_set_v9.5.fa" ftype="fasta"/>
+      </test>
+  </tests>
+  <help>
+
+.. class:: infomark
+
+**What it does**
+
+Converts file in EMBL flat format to fasta file
+  </help>
+</tool>
+