diff diamond_makedb.xml @ 0:98037ef3d2a9 draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/diamond_makedb.xml	Sun Feb 08 10:05:26 2015 -0500
@@ -0,0 +1,50 @@
+<tool id="bg_diamond_makedb" name="Diamond makedb" version="0.6.13">
+    <description>Build database from a FASTA file</description>
+    <requirements>
+        <requirement type="package" version="0.6.13">diamond</requirement>
+    </requirements>
+    <command>
+    <!-- DB has two files, *.dmnd and *.tx -->
+<![CDATA[
+    diamond makedb 
+        --threads "\${GALAXY_SLOTS:-12}"
+        --in $infile
+        --db ./database
+    &&
+    mv ./database.dmnd $outfile
+]]>
+    </command>
+    <inputs>
+        <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
+    </inputs>
+
+    <outputs>
+        <data format="diamond_database" name="outfile" label="Diamond database ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="protein.fasta" ftype="fasta"/>
+            <output name="outfile" file="diamond_makedb_result1.dmnd" ftpye="diamond_database"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
+On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
+about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500
+times faster than BLASTX, finding more than 94% of all matches.
+
+.. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
+
+
+]]>
+    </help>
+    <citations>
+        <citation type="doi">10.1038/nmeth.3176</citation>
+    </citations>
+</tool>