diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 371e66dbde5..9baf44c550a 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -52,7 +52,7 @@
     <tool file="maf/maf_to_interval.xml" /> 
     <tool file="maf/maf_to_fasta.xml" />
     <tool file="fasta_tools/tabular_to_fasta.xml" />
-    <tool file="fastx_toolkit/fastq_to_fasta.xml" />
+    <tool file="fastq/fastq_to_fasta.xml" />
   </section>
   <section name="FASTA manipulation" id="fasta_manipulation">
     <tool file="fasta_tools/fasta_compute_length.xml" />
@@ -289,7 +289,9 @@
         <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="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" />
diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index b3a5ed6217b..f6e9f86ad91 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -80,7 +80,7 @@
     <tool file="maf/maf_to_interval.xml" />
     <tool file="maf/maf_to_fasta.xml" />
     <tool file="fasta_tools/tabular_to_fasta.xml" />
-    <tool file="fastx_toolkit/fastq_to_fasta.xml" />
+    <tool file="fastq/fastq_to_fasta.xml" />
     <tool file="filters/wiggle_to_simple.xml" />
     <tool file="filters/sff_extractor.xml" />
     <tool file="filters/gtf2bedgraph.xml" />
@@ -212,7 +212,9 @@
         <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="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" />