Mercurial > repos > jjohnson > contig_annotation_tool

annotate cat_summarise.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
parents 18ece3d5bcde
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1 <tool id="cat_summarise" name="CAT summarise" 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 summarise -c '$contigs_fasta' -i '$input'
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10 -o output_names_summary.txt
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11 && @TXT2TSV@ -i output_names_summary.txt -o $output
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12 ]]></command>
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13 <inputs>
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14 <param argument="--input" type="data" format="tabular" label="classification.official_names.txt"
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15 help="The classication must be made with only_official names"/>
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16 <param argument="--contigs_fasta" type="data" format="fasta" optional="true" label="contigs.fasta"
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17 help="Required if a contig2classification.names"/>
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18 </inputs>
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19 <outputs>
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20 <data name="output" format="tabular"/>
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21 </outputs>
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22 <tests>
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23 <test>
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24 <param name="input" ftype="tabular" value="test_contig.contig2classification.names.txt"/>
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25 <param name="contigs_fasta" ftype="fasta" value="contigs.fasta"/>
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26 <output name="output">
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27 <assert_contents>
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28 <has_text text="Firmicutes" />
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29 </assert_contents>
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30 </output>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 **CAT summarise**
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35
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36 Summarise taxonomic asignemts from anamed CAT or BAT classification file.
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37
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38 Required arguments:
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39 -i, --input_file Path to named CAT contig classification file or BAT
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40 bin classification file. Currently only official ranks
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41 are supported, and only classification files
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42 containing a single classification per contig / bin.
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43
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44 Optional arguments:
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45 -c, --contigs_fasta
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46 Path to contigs fasta file. This is required if you
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47 want to summarise a contig classification file.
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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>