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author devteam
date Mon, 21 Mar 2016 12:07:33 -0400
parents 77ca66b1f5e9
children b9971bca4b01
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1 <tool id="kraken-translate" name="Kraken-translate" version="1.2.0">
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2 <description>
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3 convert taxonomy IDs to names
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command>
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12 <![CDATA[
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13 @SET_DATABASE_PATH@ &&
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14 kraken-translate @INPUT_DATABASE@ $mpa_format "${input}" > "${translated}"
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15 ]]>
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16 </command>
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17 <inputs>
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18 <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
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19 <param label="Restrict labels to standard rank assignments" name="mpa_format" truevalue="--mpa-format" falsevalue="" type="boolean" />
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20 <expand macro="input_database" />
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21 </inputs>
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22 <outputs>
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23 <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input" value="kraken_translate_test1.tab" ftype="tabular"/>
475284b74179 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 3abfc7eb2999fa588862b84c453012c811fa8350
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28 <param name="mpa-format" value="false"/>
475284b74179 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 3abfc7eb2999fa588862b84c453012c811fa8350
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29 <param name="kraken_database" value="test_db"/>
475284b74179 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 3abfc7eb2999fa588862b84c453012c811fa8350
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30 <output name="translated" file="kraken_translate_test1_output.tab" ftype="tabular"/>
475284b74179 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit 3abfc7eb2999fa588862b84c453012c811fa8350
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31 </test>
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32 </tests>
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33 <help>
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34 <![CDATA[
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36 .. class:: warningmark
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38 **Note**: the database used must be the same as the one used in the original Kraken run
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40 -------
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42 **What it does**
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44 The file sequences.labels generated by the above example is a text file with two tab-delimited columns, and one line for each classified sequence in sequences.fa; unclassified sequences are not reported by kraken-translate. The first column of kraken-translate's output are the sequence IDs of the classified sequences, and the second column contains the taxonomy of the sequence. For example, an output line from kraken::
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46 C SEQ1 562 36 562:6
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48 Would result in a corresponding output line from kraken-translate::
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49
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50 SEQ1 root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli
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52 Alternatively, kraken-translate accepts the option ``--mpa-format`` which will report only levels of the taxonomy with standard rank assignments (superkingdom, kingdom, phylum, class, order, family, genus, species), and uses pipes to delimit the various levels of the taxonomy. For example, ``kraken-translate --mpa-format`` with the above example output from kraken would result in the following line of output::
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54 SEQ1 d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli
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56 Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate.
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57 ]]>
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58 </help>
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59 <expand macro="citations" />
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60 </tool>