diff --git a/tool_conf.xml.sample b/tool_conf.xml.sample
index d23b24b1362..6006e6f0b42 100644
--- a/tool_conf.xml.sample
+++ b/tool_conf.xml.sample
@@ -316,7 +316,7 @@
     <tool file="fasta_tools/fasta_filter_by_length/1.0.0/fasta_filter_by_length.xml" />
   </section>
   <section name="Short Read Analysis" id="short_read_analysis">
-    <tool file="metag_tools/short_reads_trim_seq.xml" />
-    <tool file="metag_tools/short_reads_figure_score.xml" />
+    <tool file="metag_tools/trim_reads/1.0.0/short_reads_trim_seq.xml" />
+    <tool file="metag_tools/quality_score_distribution/1.0.0/short_reads_figure_score.xml" />
  </section>
 </toolbox>
diff --git a/tools/metag_tools/short_reads_figure_length.py b/tools/metag_tools/array_of_reads_length/1.0.0/short_reads_figure_length.py
similarity index 100%
rename from tools/metag_tools/short_reads_figure_length.py
rename to tools/metag_tools/array_of_reads_length/1.0.0/short_reads_figure_length.py
diff --git a/tools/metag_tools/short_reads_figure_length.xml b/tools/metag_tools/array_of_reads_length/1.0.0/short_reads_figure_length.xml
similarity index 100%
rename from tools/metag_tools/short_reads_figure_length.xml
rename to tools/metag_tools/array_of_reads_length/1.0.0/short_reads_figure_length.xml
diff --git a/tools/metag_tools/blat_wrapper.py b/tools/metag_tools/blat_wrapper/1.0.0/blat_wrapper.py
similarity index 100%
rename from tools/metag_tools/blat_wrapper.py
rename to tools/metag_tools/blat_wrapper/1.0.0/blat_wrapper.py
diff --git a/tools/metag_tools/blat_wrapper.xml b/tools/metag_tools/blat_wrapper/1.0.0/blat_wrapper.xml
similarity index 100%
rename from tools/metag_tools/blat_wrapper.xml
rename to tools/metag_tools/blat_wrapper/1.0.0/blat_wrapper.xml
diff --git a/tools/metag_tools/megablast_wrapper.py b/tools/metag_tools/megablast_wrapper/1.0.0/megablast_wrapper.py
similarity index 100%
rename from tools/metag_tools/megablast_wrapper.py
rename to tools/metag_tools/megablast_wrapper/1.0.0/megablast_wrapper.py
diff --git a/tools/metag_tools/megablast_wrapper.xml b/tools/metag_tools/megablast_wrapper/1.0.0/megablast_wrapper.xml
similarity index 100%
rename from tools/metag_tools/megablast_wrapper.xml
rename to tools/metag_tools/megablast_wrapper/1.0.0/megablast_wrapper.xml
diff --git a/tools/metag_tools/short_reads_figure_score.py b/tools/metag_tools/quality_score_distribution/1.0.0/short_reads_figure_score.py
similarity index 100%
rename from tools/metag_tools/short_reads_figure_score.py
rename to tools/metag_tools/quality_score_distribution/1.0.0/short_reads_figure_score.py
diff --git a/tools/metag_tools/short_reads_figure_score.xml b/tools/metag_tools/quality_score_distribution/1.0.0/short_reads_figure_score.xml
similarity index 100%
rename from tools/metag_tools/short_reads_figure_score.xml
rename to tools/metag_tools/quality_score_distribution/1.0.0/short_reads_figure_score.xml
diff --git a/tools/metag_tools/short_reads_trim_seq.py b/tools/metag_tools/trim_reads/1.0.0/short_reads_trim_seq.py
similarity index 100%
rename from tools/metag_tools/short_reads_trim_seq.py
rename to tools/metag_tools/trim_reads/1.0.0/short_reads_trim_seq.py
diff --git a/tools/metag_tools/short_reads_trim_seq.xml b/tools/metag_tools/trim_reads/1.0.0/short_reads_trim_seq.xml
similarity index 100%
rename from tools/metag_tools/short_reads_trim_seq.xml
rename to tools/metag_tools/trim_reads/1.0.0/short_reads_trim_seq.xml