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1 <tool id="bg_diamond_makedb" name="Diamond" version="0.6.13">
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2 <description>Build database from a FASTA file</description>
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3 <requirements>
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4 <requirement type="package" version="0.6.13">diamond</requirement>
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5 </requirements>
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6 <command>
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7 <!-- DB has two files, *.dmnd and *.tx -->
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8 <![CDATA[
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9 diamond makedb
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10 --threads "\${GALAXY_SLOTS:-12}"
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11 --in $infile
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12 --db $outfile
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13 ]]>
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14 </command>
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15 <inputs>
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16 <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
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17 </inputs>
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18
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19 <outputs>
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20 <data format="compressed_archive" name="outfile" label="Diamond database ${on_string}"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="infile" value="protein.fasta" ftype="fasta"/>
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25 <output name="outfile" file="diamond_makedb_result1.dmnd" ftpye="compressed_archive"/>
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26 </test>
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27 </tests>
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28 <help>
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29 <![CDATA[
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30
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31 .. class:: infomark
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32
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33 **What it does**
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34
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35 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR.
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36 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting
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37 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
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38 times faster than BLASTX, finding more than 94% of all matches.
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39
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40 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
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41
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42
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43 ]]>
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44 </help>
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45 <citations>
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46 <citation type="doi">10.1038/nmeth.3176</citation>
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47 </citations>
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48 </tool>
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