Mercurial > repos > jjohnson > contig_annotation_tool

annotate cat_add_names.xml @ 5:226949352e31 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cat commit a1c079107b72dc08612fa664897bb9d627624e52-dirty
author jjohnson
date Wed, 27 Nov 2019 12:11:14 -0500
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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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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 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>
5
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16 <param argument="--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"/>
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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>
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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
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37 Add taxonomic names to CAT or BAT output files.
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38
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39 Required arguments:
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40 -i, --input_file Path to input file. Can be either classification
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41 output file or ORF2LCA output file.
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42 -t, --taxonomy_folder Path to folder that contains taxonomy files.
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43
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44 Optional arguments:
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45 --only_official Only output official level names.
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46 --exclude_scores Do not include bit-score support scores in the
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47 lineage.
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48
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49 @COMMON_HELP@
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50 ]]></help>
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51 <expand macro="citations" />
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52 </tool>