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annotate kraken-translate.xml @ 5:473f01651106 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit c5dd035dbee6021f3555755cf4c814e760cecd09
author devteam
date Wed, 23 Mar 2016 11:02:11 -0400
parents e190a178e49f
children e44e186320d7
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473f01651106 planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit c5dd035dbee6021f3555755cf4c814e760cecd09
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1 <tool id="kraken-translate" name="Kraken-translate" version="1.2.1">
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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"/>
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28 <param name="mpa-format" value="false"/>
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29 <param name="kraken_database" value="test_db"/>
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30 <output name="translated" file="kraken_translate_test1_output.tab" ftype="tabular"/>
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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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41
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42 **What it does**
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43
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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>