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1 <tool id="blastxml_to_top_descr" name="BLAST top hit descriptions" version="0.0.1">
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2 <description>Make a table from BLAST XML</description>
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3 <command interpreter="python">
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4 blastxml_to_top_descr.py $blastxml_file $tabular_file $topN
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5 </command>
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6 <inputs>
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7 <param name="blastxml_file" type="data" format="blastxml" label="BLAST results as XML"/>
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8 <param name="topN" type="integer" min="1" max="100" optional="false" label="Number of descriptions" value="3"/>
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9 </inputs>
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10 <outputs>
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11 <data name="tabular_file" format="tabular" label="Top $topN descriptions from $blastxml_file.name" />
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12 </outputs>
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13 <requirements>
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14 </requirements>
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15 <tests>
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16 <test>
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17 <param name="blastxml_file" value="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
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18 <param name="topN" value="3" />
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19 <output name="tabular_file" file="blastp_four_human_vs_rhodopsin_top3.tabular" ftype="tabular" />
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20 </test>
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21 </tests>
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22 <help>
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23
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24 **What it does**
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25
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26 NCBI BLAST+ (and the older NCBI 'legacy' BLAST) can output in a range of
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27 formats including text, tabular and a more detailed XML format. You can
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28 do a lot of things with tabular files in Galaxy (sorting, filtering, joins,
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29 etc) however currently the BLAST tabular output omits the hit descriptions
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30 found in the other output formats.
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31
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32 This tool turns a BLAST XML file into a simple tabular file containing
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33 one row per query sequence, containing the query identifier and then
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34 the three (by default) top hit descriptions. If a query doesn't have
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35 that many hits, then these entries are left blank.
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36
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37 **Example Usage**
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38
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39 One simple usage would be to take a transcriptome assembly or set of
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40 gene predictions, run a BLAST search against the NCBI NR database, and
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41 then use this tool to make a table of the top three BLAST hits. This
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42 can give you a 'quick and dirty' crude annotation, potentially enough
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43 to spot some problems (e.g. bacterial contaimination could be very
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44 obvious).
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45
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46 </help>
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47 </tool>
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