Mercurial > repos > jjohnson > contig_annotation_tool

annotate cat_add_names.xml @ 0:ad7507073c3f draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
author jjohnson
date Sun, 24 Nov 2019 21:56:00 -0500
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children 226949352e31
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ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
jjohnson
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1 <tool id="cat_add_names" name="CAT add_names" version="@VERSION@.0">
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2 <description>annotate with taxonomic classification</description>
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jjohnson
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3 <macros>
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jjohnson
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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 CAT add_names -i '$input'
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10 @CAT_TAXONOMY@
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11 @ADD_NAMES_OPTIONS@
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12 -o output_names.txt
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13 && @TXT2TSV@ -i output_names.txt -o $output
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14 ]]></command>
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15 <inputs>
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16 <param name="input" type="data" format="tabular,txt" label="classification.txt or ORF2LCA.txt"/>
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17 <expand macro="cat_db" />
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18 <expand macro="add_names_options" />
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19 </inputs>
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20 <outputs>
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21 <data name="output" format="tabular"/>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input" ftype="tabular" value="test_contig.contig2classification.txt"/>
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26 <expand macro="test_catdb"/>
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27 <output name="output">
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28 <assert_contents>
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29 <has_text text="Firmicutes" />
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30 </assert_contents>
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31 </output>
ad7507073c3f planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit f80f020c77d04c2e13b89aaea3d784314b940931-dirty
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 **CAT/BAT add_names**
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36 Add names for the NCBI taxomy IDs.
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37
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38 @COMMON_HELP@
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39 ]]></help>
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40 <expand macro="citations" />
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41 </tool>