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comparison kraken-translate.xml @ 3:443674e0ca7f draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
author devteam
date Fri, 18 Dec 2015 19:41:51 -0500
parents a080250b8326
children e190a178e49f
comparison
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2:a080250b8326 3:443674e0ca7f
3 convert taxonomy IDs to names 3 convert taxonomy IDs to names
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements" />
9 <expand macro="stdio" />
10 <expand macro="version_command" />
8 <command> 11 <command>
9 <![CDATA[ 12 <![CDATA[
10 @SET_DATABASE_PATH@ && 13 @SET_DATABASE_PATH@ &&
11 kraken-translate @INPUT_DATABASE@ $mpa_format "${input}" > "${translated}" 14 kraken-translate @INPUT_DATABASE@ $mpa_format "${input}" > "${translated}"
12 ]]> 15 ]]>
17 <expand macro="input_database" /> 20 <expand macro="input_database" />
18 </inputs> 21 </inputs>
19 <outputs> 22 <outputs>
20 <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" /> 23 <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />
21 </outputs> 24 </outputs>
25 <tests>
26 <test>
27 <param name="input" value="kraken_translate_test1.tab" ftype="tabular"/>
28 <param name="mpa-format" value="false"/>
29 <param name="kraken_database" value="test_db"/>
30 <output name="translated" file="kraken_translate_test1_output.tab" ftype="tabular"/>
31 </test>
32 </tests>
22 <help> 33 <help>
23 <![CDATA[ 34 <![CDATA[
24 35
25 .. class:: warningmark 36 .. class:: warningmark
26 37
43 SEQ1 d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli 54 SEQ1 d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli
44 55
45 Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate. 56 Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate.
46 ]]> 57 ]]>
47 </help> 58 </help>
48 <expand macro="requirements" />
49 <expand macro="stdio" />
50 <expand macro="version_command" />
51 <expand macro="citations" /> 59 <expand macro="citations" />
52 </tool> 60 </tool>