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annotate kraken-translate.xml @ 2:a080250b8326 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
author devteam
date Wed, 15 Jul 2015 15:22:31 -0400
parents f23c90363093
children 443674e0ca7f
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a080250b8326 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
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1 <tool id="kraken-translate" name="Kraken-translate" version="1.1.0">
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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 <command>
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9 <![CDATA[
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10 @SET_DATABASE_PATH@ &&
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11 kraken-translate @INPUT_DATABASE@ $mpa_format "${input}" > "${translated}"
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12 ]]>
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13 </command>
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14 <inputs>
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15 <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
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16 <param label="Restrict labels to standard rank assignments" name="mpa_format" truevalue="--mpa-format" falsevalue="" type="boolean" />
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17 <expand macro="input_database" />
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18 </inputs>
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19 <outputs>
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20 <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />
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21 </outputs>
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22 <help>
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23 <![CDATA[
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a080250b8326 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
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a080250b8326 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
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25 .. class:: warningmark
a080250b8326 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
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27 **Note**: the database used must be the same as the one used in the original Kraken run
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29 -------
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30
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31 **What it does**
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33 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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35 C SEQ1 562 36 562:6
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37 Would result in a corresponding output line from kraken-translate::
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39 SEQ1 root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli
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41 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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43 SEQ1 d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli
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45 Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate.
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46 ]]>
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47 </help>
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48 <expand macro="requirements" />
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49 <expand macro="stdio" />
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50 <expand macro="version_command" />
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51 <expand macro="citations" />
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52 </tool>