--- a/renameSequences.xml	Thu Jul 27 09:46:13 2023 +0000
+++ b/renameSequences.xml	Wed Aug 02 11:31:12 2023 +0000
@@ -1,25 +1,38 @@
-<tool id="rename_sequences" name="Rename sequences" version="1.0.0">
-<description> Rename sequences using numerical counter, keep required prefix and pair information </description>
-<command interpreter="python">
-renameSequences2.py $input $paired index.tmp $prefix_length > $output
-</command>
+<tool id="rename_sequences" name="Rename sequences" version="1.0.0.3">
+    <description>Rename sequences using numerical counter, keep required prefix and pair
+        information
+    </description>
+    <required_files>
+        <include type="literal" path="renameSequences2.py"/>
+    </required_files>
+    <command>
+        python '$__tool_directory__'/renameSequences2.py $input $paired index.tmp
+        $prefix_length > $output
+    </command>
 
- <inputs>
-  <param format="fasta" type="data" name="input" label="Choose your FASTA file" />
-  <param name="prefix_length" type="integer" size="10" value="0" label="Prefix length" help="Enter the length of prefix to keep in sequences names" />
-  <param name="paired" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Sequences are paired-end reads in interlaced format" help=""/>
- </inputs>
+    <inputs>
+        <param format="fasta" type="data" name="input" label="Choose your FASTA file"/>
+        <param name="prefix_length" type="integer" size="10" value="0"
+               label="Prefix length"
+               help="Enter the length of prefix to keep in sequences names"/>
+        <param name="paired" type="boolean" truevalue="true" falsevalue="false"
+               checked="False" label="Sequences are paired-end reads in interlaced format"
+               help=""/>
+    </inputs>
 
 
- <outputs>
- 	<data format="fasta" name="output" label="Renamed sequences from dataset ${input.hid}" />
- </outputs>
+    <outputs>
+        <data format="fasta" name="output"
+              label="Renamed sequences from dataset ${input.hid}"/>
+    </outputs>
+
+    <help>
+        **What is does**
 
- <help>
-**What is does**
- 
-Use this tool to rename your sequences with numerical counter while keeping sequence name prefex as part of the name. 
-If paired-end reads are used, the last character in sequence name is used to distinguish pairs.  
- 
-</help>
+        Use this tool to rename your sequences with numerical counter while keeping
+        sequence name prefex as part of the name.
+        If paired-end reads are used, the last character in sequence name is used to
+        distinguish pairs.
+
+    </help>
 </tool>