diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 04aca800255..3ad306b1422 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -55,6 +55,7 @@
   <section id="convert" name="Convert Formats">
     <tool file="filters/bed2gff.xml" />
     <tool file="fasta_tools/fasta_to_tabular.xml" />
+    <tool file="fastq/fastq_to_fasta.xml" />
     <tool file="filters/gff2bed.xml" />
     <tool file="maf/maf_to_bed.xml" />
     <tool file="maf/maf_to_interval.xml" />
@@ -226,6 +227,7 @@
         <tool file="fastq/fastq_trimmer_by_quality.xml" />
         <tool file="fastq/fastq_masker_by_quality.xml" />
         <tool file="fastq/fastq_manipulation.xml" />
+        <tool file="fastq/fastq_to_fasta.xml" />
         <tool file="fastq/fastq_to_tabular.xml" />
         <tool file="fastq/tabular_to_fastq.xml" />
     <label id="fastx_toolkit_fastq" text="FASTX-Toolkit for FASTQ data" />