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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3873b52450c86190e4fb8767cffe5730d6e37692"
author iuc
date Sat, 27 Nov 2021 10:11:18 +0000 (2021-11-27)
parents e0458a8ae67b
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1 <tool id="kraken-translate" name="Kraken-translate" version="@WRAPPER_VERSION@">
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2 <description>convert taxonomy IDs to names</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 @SET_DATABASE_PATH@ &&
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11 kraken-translate
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12 @INPUT_DATABASE@
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13 $mpa_format
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14 '${input}'
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15 > '${translated}'
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16 ]]></command>
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17 <inputs>
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18 <param name="input" type="data" format="tabular" label="Kraken output"
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19 help="Select taxonomy classification produced by kraken"/>
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20 <param name="mpa_format" type="boolean" truevalue="--mpa-format" falsevalue=""
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21 label="Restrict labels to standard rank assignments" />
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22
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23 <expand macro="input_database" />
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24 </inputs>
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25 <outputs>
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26 <data name="translated" format="tabular" label="${tool.name} on ${on_string}: Translated classification"/>
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="input" value="kraken-translate/kraken_translate_test1.tab" ftype="tabular"/>
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31 <param name="mpa_format" value="false"/>
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32 <param name="kraken_database" value="new_style_test_entry"/>
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33 <output name="translated" file="kraken-translate/kraken_translate_test1_output.tab" ftype="tabular"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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38 .. class:: warningmark
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40 **Note**: the database used must be the same as the one used in the original Kraken run
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42 -------
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43
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44 **What it does**
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45
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46 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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48 C SEQ1 562 36 562:6
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50 Would result in a corresponding output line from kraken-translate::
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52 SEQ1 root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli
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54 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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56 SEQ1 d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli
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58 Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate.
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59 ]]></help>
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60 <expand macro="citations" />
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61 </tool>