--- a/fargene.xml	Mon Dec 02 04:39:18 2019 -0500
+++ b/fargene.xml	Fri Feb 09 21:30:09 2024 +0000
@@ -3,6 +3,9 @@
     <macros>
         <import>macros.xml</import>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">fargene</xref>
+    </xrefs>
     <expand macro="requirements" />
     <version_command>fargene --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
@@ -102,24 +105,17 @@
             <option value="class_d_2">Class D beta-lactamases-2</option>
             <option value="qnr">QNR</option>
         </param>
-        <param name="score" argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as
-                        a (almost) complete gene" />
-        <param name="meta_score" argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as
-                        a positive. Expressed as score per amino acid" />
-        <param name="protein" argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" />
-        <param name="min_orf_length" argument="--min-orf-length" type="integer" min="1" value="90" label="The minimal length for a retrieved predicted ORF (nt)" />
-        <param name="retrieve_whole" argument="--retrieve-whole" type="boolean" truevalue="--retrieve-whole " falsevalue="" checked="False" label="Use this flag if the whole sequence where a hit is
-                        detected should be retrieved" />
-        <param name="no_orf_predict" argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" />
-        <param name="no_quality_filtering" argument="--no-quality-filtering" type="boolean" truevalue="--no-quality-filtering" falsevalue="" checked="False" label="Use if no quality control should be performed on the
-                        metagenomic data" />
-        <param name="no_assembly" argument="--no-assembly" type="boolean" truevalue="--no-assembly" falsevalue="" checked="False" label="Use if you want to skip the assembly and retrieval of
-                        contigs for metagenomic data" />
-        <param name="orf_finder" argument="--orf-finder" type="boolean" truevalue="--orf-finder" falsevalue="" checked="False" label="Use NCBI ORFfinder instead of prodigal for ORF
-                        prediction of genomes/contigs" />
-        <param name="store_peptides" argument="--store-peptides" type="boolean" truevalue="--store-peptides" falsevalue="" checked="False" label="Store the translated sequences. Useful if you plan to
-                        redo the analysis using a different model and want to
-                        skip the preprocessing steps" />
+        <param argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as a (almost) complete gene" />
+        <param argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as a positive. Expressed as score per amino acid" />
+        <param argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" />
+        <param argument="--min-orf-length" type="integer" min="1" value="90" label="The minimal length for a retrieved predicted ORF (nt)" />
+        <param argument="--retrieve-whole" type="boolean" truevalue="--retrieve-whole " falsevalue="" checked="False" label="Use this flag if the whole sequence where a hit is detected should be retrieved" />
+        <param argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" />
+        <param argument="--no-quality-filtering" type="boolean" truevalue="--no-quality-filtering" falsevalue="" checked="False" label="Use if no quality control should be performed on the metagenomic data" />
+        <param argument="--no-assembly" type="boolean" truevalue="--no-assembly" falsevalue="" checked="False" label="Use if you want to skip the assembly and retrieval of contigs for metagenomic data" />
+        <param argument="--orf-finder" type="boolean" truevalue="--orf-finder" falsevalue="" checked="False" label="Use NCBI ORFfinder instead of prodigal for ORF prediction of genomes/contigs" />
+        <param argument="--store-peptides" type="boolean" truevalue="--store-peptides" falsevalue="" checked="False" label="Store the translated sequences" 
+            help="Useful if you plan to redo the analysis using a different model and want to skip the preprocessing steps" />
 
     </inputs>
     <outputs>