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comparison kraken-translate.xml @ 3:9bdcba262627 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_translate/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
author iuc
date Mon, 07 Aug 2017 17:29:45 -0400
parents b9971bca4b01
children 9a5be5b1a5c9
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2:b9971bca4b01 3:9bdcba262627
1 <tool id="kraken-translate" name="Kraken-translate" version="1.2.1"> 1 <tool id="kraken-translate" name="Kraken-translate" version="@WRAPPER_VERSION@">
2 <description> 2 <description>convert taxonomy IDs to names</description>
3 convert taxonomy IDs to names
4 </description>
5 <macros> 3 <macros>
6 <import>macros.xml</import> 4 <import>macros.xml</import>
7 </macros> 5 </macros>
8 <expand macro="requirements" /> 6 <expand macro="requirements" />
9 <expand macro="stdio" />
10 <expand macro="version_command" /> 7 <expand macro="version_command" />
11 <command> 8 <command detect_errors="exit_code"><![CDATA[
12 <![CDATA[
13 @SET_DATABASE_PATH@ && 9 @SET_DATABASE_PATH@ &&
14 kraken-translate @INPUT_DATABASE@ $mpa_format "${input}" > "${translated}" 10
15 ]]> 11 kraken-translate
16 </command> 12 @INPUT_DATABASE@
13 $mpa_format
14 '${input}'
15 > '${translated}'
16 ]]></command>
17 <inputs> 17 <inputs>
18 <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/> 18 <param name="input" type="data" format="tabular" label="Kraken output"
19 <param label="Restrict labels to standard rank assignments" name="mpa_format" truevalue="--mpa-format" falsevalue="" type="boolean" /> 19 help="Select taxonomy classification produced by kraken"/>
20 <param name="mpa_format" type="boolean" truevalue="--mpa-format" falsevalue=""
21 label="Restrict labels to standard rank assignments" />
22
20 <expand macro="input_database" /> 23 <expand macro="input_database" />
21 </inputs> 24 </inputs>
22 <outputs> 25 <outputs>
23 <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" /> 26 <data name="translated" format="tabular" label="${tool.name} on ${on_string}: Translated classification"/>
24 </outputs> 27 </outputs>
25 <tests> 28 <tests>
26 <test> 29 <test>
27 <param name="input" value="kraken_translate_test1.tab" ftype="tabular"/> 30 <param name="input" value="kraken_translate_test1.tab" ftype="tabular"/>
28 <param name="mpa-format" value="false"/> 31 <param name="mpa-format" value="false"/>
29 <param name="kraken_database" value="test_db"/> 32 <param name="kraken_database" value="test_db"/>
30 <output name="translated" file="kraken_translate_test1_output.tab" ftype="tabular"/> 33 <output name="translated" file="kraken_translate_test1_output.tab" ftype="tabular"/>
31 </test> 34 </test>
32 </tests> 35 </tests>
33 <help> 36 <help><![CDATA[
34 <![CDATA[
35 37
36 .. class:: warningmark 38 .. class:: warningmark
37 39
38 **Note**: the database used must be the same as the one used in the original Kraken run 40 **Note**: the database used must be the same as the one used in the original Kraken run
39 41
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:: 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::
53 55
54 SEQ1 d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli 56 SEQ1 d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli
55 57
56 Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate. 58 Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate.
57 ]]> 59 ]]></help>
58 </help>
59 <expand macro="citations" /> 60 <expand macro="citations" />
60 </tool> 61 </tool>