diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 5c2460c58f2..503b33a8ae2 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -305,15 +305,6 @@
         <tool file="fastq/fastq_paired_end_splitter.xml" />
         <tool file="fastq/fastq_paired_end_joiner.xml" />
         <tool file="fastq/fastq_stats.xml" />
-    <!--<label text="Deprecated: Generic FASTQ data" id="fastq" />
-        <tool file="next_gen_conversion/fastq_gen_conv.xml" />
-        <tool file="fastx_toolkit/fastq_quality_converter.xml" />
-        <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
-        <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
-        <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
-        <tool file="metag_tools/split_paired_reads.xml" /> 
-        <tool file="fastx_toolkit/fastq_to_fasta.xml" />
-    -->
     <label text="Roche-454 data" id="454" />
         <tool file="metag_tools/short_reads_figure_score.xml" />
         <tool file="metag_tools/short_reads_trim_seq.xml" />
@@ -331,6 +322,21 @@
         <tool file="fastq/fastq_to_fasta.xml" />
         <tool file="fastq/fastq_to_tabular.xml" />
         <tool file="fastq/tabular_to_fastq.xml" />
+    <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit_fastq" />
+        <tool file="fastx_toolkit/fastq_quality_converter.xml" />
+        <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
+        <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
+        <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
+        <tool file="fastx_toolkit/fastq_to_fasta.xml" />
+        <tool file="fastx_toolkit/fastq_quality_filter.xml" />
+        <tool file="fastx_toolkit/fastq_to_fasta.xml" />
+        <tool file="fastx_toolkit/fastx_artifacts_filter.xml" />
+        <tool file="fastx_toolkit/fastx_barcode_splitter.xml" />
+        <tool file="fastx_toolkit/fastx_clipper.xml" />
+        <tool file="fastx_toolkit/fastx_collapser.xml" />
+        <tool file="fastx_toolkit/fastx_renamer.xml" />
+        <tool file="fastx_toolkit/fastx_reverse_complement.xml" />
+        <tool file="fastx_toolkit/fastx_trimmer.xml" />
   </section>
   <section name="NGS: Mapping" id="ngs_mapping">
     <label text="Illumina" id="illumina"/>
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index dfd49e3ffdc..884470f4992 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -218,15 +218,6 @@
         <tool file="fastq/fastq_paired_end_splitter.xml" />
         <tool file="fastq/fastq_paired_end_joiner.xml" />
         <tool file="fastq/fastq_stats.xml" />
-    <!--<label text="Deprecated: Generic FASTQ data" id="fastq" />
-        <tool file="next_gen_conversion/fastq_gen_conv.xml" />
-        <tool file="fastx_toolkit/fastq_quality_converter.xml" />
-        <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
-        <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
-        <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
-        <tool file="metag_tools/split_paired_reads.xml"
-        <tool file="fastx_toolkit/fastq_to_fasta.xml" />
-    -->
     <label text="Roche-454 data" id="454" />
         <tool file="metag_tools/short_reads_figure_score.xml" />
         <tool file="metag_tools/short_reads_trim_seq.xml" />
@@ -244,6 +235,21 @@
         <tool file="fastq/fastq_to_fasta.xml" />
         <tool file="fastq/fastq_to_tabular.xml" />
         <tool file="fastq/tabular_to_fastq.xml" />
+    <label text="FASTX-Toolkit for FASTQ data" id="fastx_toolkit" />
+        <tool file="fastx_toolkit/fastq_quality_converter.xml" />
+        <tool file="fastx_toolkit/fastx_quality_statistics.xml" />
+        <tool file="fastx_toolkit/fastq_quality_boxplot.xml" />
+        <tool file="fastx_toolkit/fastx_nucleotides_distribution.xml" />
+        <tool file="fastx_toolkit/fastq_to_fasta.xml" />
+        <tool file="fastx_toolkit/fastq_quality_filter.xml" />
+        <tool file="fastx_toolkit/fastq_to_fasta.xml" />
+        <tool file="fastx_toolkit/fastx_artifacts_filter.xml" />
+        <tool file="fastx_toolkit/fastx_barcode_splitter.xml" />
+        <tool file="fastx_toolkit/fastx_clipper.xml" />
+        <tool file="fastx_toolkit/fastx_collapser.xml" />
+        <tool file="fastx_toolkit/fastx_renamer.xml" />
+        <tool file="fastx_toolkit/fastx_reverse_complement.xml" />
+        <tool file="fastx_toolkit/fastx_trimmer.xml" />  
   </section>
   <!--
   Keep this section commented until it includes tools that