Commits

Anonymous committed 8e45646

added annovar tool into the tool panel and table data

Comments (0)

Files changed (2)

     <tool file="tool_installer/repo_installer.xml"/>
     <tool file="tool_installer/tool_info_grabber.xml"/>
   </section>
+
   <label text="Data Transfer" id="data_transfer" />
   <section name="Globus Data Transfer" id="globus">
     <tool file="globus/from_go.xml" />
   <section name="NGS: RNA Analysis" id="ngs-rna-tools">
     <label text="Transcriptome Alignment" id="rna_seq_alignment" />
     <tool file="ngs_rna/tophat_wrapper.xml" />
-    <tool file="ngs_rna/tophat2_wrapper.xml" />
     <tool file="ngs_rna/tophat_color_wrapper.xml" />
-    <tool file="rsem/rsem-1.1.17.xml" />
     <label text="Cufflinks Package " id="rna_seq_tools" />
     <tool file="ngs_rna/cufflinks_wrapper.xml" />
     <tool file="ngs_rna/cuffcompare_wrapper.xml" />
     <tool file="annotate_variants/seattleSNPparser.xml" />
     <tool file="annotate_variants/snp_Annotated2xmlV3.xml" />
     <tool file="seattleseq/seattleseq.xml"/>
+    <tool file="annovar/annovar.xml"/>
   </section>
 
   <section name="NGS: CGA Tools" id="CGA_tools">

tool_data_table_conf.xml

         <columns>value, dbkey, name, path</columns>
         <file path="/mnt/galaxyIndices/galaxy/tool-data/picard_index.loc" />
     </table>
+    <!-- Location of Picard dict files valid for GATK -->
+    <table name="gatk2_picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/mnt/galaxyIndices/galaxy/tool-data/picard_index.loc" />
+    </table>
     <!-- Available of GATK references -->
     <table name="gatk_annotations" comment_char="#">
         <columns>value, name, gatk_value, tools_valid_for</columns>
         <file path="tool-data/gatk_annotations.txt" />
     </table>
-    <!-- Location of Picard dict files valid for GATK -->
-    <table name="gatk2_picard_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="/mnt/galaxyIndices/galaxy/tool-data/picard_index.loc" />
-    </table>
     <!-- Available of GATK references -->
     <table name="gatk2_annotations" comment_char="#">
         <columns>value, name, gatk_value, tools_valid_for</columns>
         <columns>value, dbkey, name, path</columns>
         <file path="tool-data/novoalign_indices.loc" />
     </table>
+    <!-- ANNOVAR files -->
+    <table name="annovar_loc" comment_char="#">
+        <columns>value, dbkey, name, ANNOVAR_scripts, ANNOVAR_humandb</columns>
+        <file path="tool-data/annovar.loc" /> 
+    </table>
 </tables>