Adding basic tblastn wrapper

tool_conf.xml.sample

@@ -264,6 +264,7 @@
   -->
   <section name="NCBI BLAST+" id="ncbi_blast_plus_tools">
    <tool file="ncbi_blast_plus/ncbi_blastn_wrapper.xml" />
+   <tool file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml" />
    <tool file="ncbi_blast_plus/ncbi_blastp_wrapper.xml" />
    <tool file="ncbi_blast_plus/blast_filter_fasta.xml" />
   </section>

tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml

@@ -0,0 +1,97 @@
+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.1">
+    <description>Search translated nucleotide database with protein query sequence(s)</description>
+    <command>
+      tblastn
+       -query "$query"
+       -db "$database"
+       -evalue $evalue_cutoff
+       -seg $adv_opts.filter_query
+       -out $output1
+       -outfmt $out_format
+       -num_threads 8
+    </command>
+    <inputs>
+        <param name="query" type="data" format="fasta" label="Query sequence(s)"/> 
+        <param name="database" type="select" display="radio" label="Nucelotide BLAST database">
+            <options from_file="blastdb.loc">
+              <column name="name" index="0"/>
+              <column name="value" index="1"/>
+            </options>
+        </param>
+        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" />
+        <param name="out_format" type="select" label="Output format">
+            <option value="6">Tabular</option>
+            <option value="5">BLAST XML</option>
+            <option value="0">Pairwise text</option>
+            <!--
+            <option value="11">BLAST archive format (ASN.1)</option>
+            -->
+        </param>
+        <conditional name="adv_opts">
+            <param name="adv_opts_selector" type="select" label="Advanced Options">
+              <option value="basic" selected="True">Hide Advanced Options</option>
+              <option value="advanced">Show Advanced Options</option>
+            </param>
+            <when value="basic">
+                <param name="filter_query" type="hidden" value="yes" />
+            </when>
+            <when value="advanced">
+                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <!-- TODO, can I get the caption rather than the value? e.g. 'NT' rather than a long path? -->
+        <data name="output1" format="tabular" label="tblastn on ${database.value_label}">
+            <change_format>
+                <when input="out_format" value="0" format="txt"/>
+            </change_format>
+            <change_format>
+                <when input="out_format" value="5" format="blastxml"/>
+            </change_format>
+        </data>
+    </outputs>
+    <requirements>
+        <requirement type="binary">blastn</requirement>
+    </requirements>
+    <tests>
+    </tests>
+    <help>
+    
+.. class:: warningmark
+
+**Note**. Database searches may take substantial amount of time. For large input datasets it is advisable to allow overnight processing.  
+
+-----
+
+**What it does**
+
+This tool runs NCBI BLAST+ tblastn tool.
+
+-----
+
+**Output format**
+
+The default Output of this tool is tabular, containing 12 columns:
+
+1. Id of your sequence 
+2. GI of the database hit 
+3. % identity
+4. Alignment length
+5. # mismatches
+6. # gaps
+7. Start position in your sequence
+8. End position in your sequence
+9. Start position in database hit
+10. End position in database hit
+11. E-value
+12. Bit score
+
+-------
+
+**References**
+
+Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
+
+    </help>
+</tool>