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annotate diamond_makedb.xml @ 4:cc30b68c0495 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b193689f9f30ce65a77be2d2c00929e3335a7d82
author bgruening
date Wed, 26 Jul 2017 17:26:18 -0400
parents df7738595640
children 64be1ac21109
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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1 <tool id="bg_diamond_makedb" name="Diamond makedb" version="@VERSION@">
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2 <description>Build database from a FASTA file</description>
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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3 <macros>
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4 <import>macros.xml</import>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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5 </macros>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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7 <expand macro="requirements" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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8 <expand macro="stdio" />
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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9 <expand macro="version_command" />
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10
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11 <command>
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12 <!-- DB has two files, *.dmnd and *.tx -->
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13 <![CDATA[
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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14 diamond makedb
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15 --threads "\${GALAXY_SLOTS:-12}"
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16 --in '$infile'
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17 --db ./database
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18 ]]>
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19 </command>
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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20
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21 <inputs>
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22 <param name="infile" type="data" format="fasta" label="Input reference file in FASTA format" />
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23 </inputs>
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24
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25 <outputs>
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26 <data format="dmnd" name="outfile" from_work_dir="database.dmnd" label="${tool.name} on ${on_string}"/>
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27 </outputs>
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28
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29 <tests>
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30 <test>
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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31 <param name="infile" value="db.fasta" ftype="fasta"/>
df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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32 <output name="outfile" value="db.dmnd"/>
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33 </test>
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34 </tests>
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35
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36 <help>
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37 <![CDATA[
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38
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39 .. class:: infomark
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40
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41 **What it does**
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42
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43 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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44 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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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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45 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND is about 2,500
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46 times faster than BLASTX, finding more than 94% of all matches.
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47
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48 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
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51 ]]>
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52 </help>
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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df7738595640 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
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54 <expand macro="citations" />
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55 </tool>