Mercurial > repos > iuc > concoct_coverage_table

annotate coverage_table.xml @ 1:aff48b4c0ecc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 77dea70f156d56c83b6851b61dc997d2b344bdc9
author iuc
date Fri, 01 Jul 2022 14:11:37 +0000
parents 53f2fabb9d7d
children
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53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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1 <tool id="concoct_coverage_table" name="CONCOCT coverage table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description></description>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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3 <macros>
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4 <import>macros.xml</import>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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5 </macros>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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6 <expand macro="requirements"/>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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7 <command detect_errors="exit_code"><![CDATA[
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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8 python '$__tool_directory__/coverage_table.py'
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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9 --input_fasta '$input_fasta'
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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10 #if $input_fasta.is_of_type('fasta.gz'):
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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11 --gzipped
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12 #end if
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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13 --input_tabular '$input_tabular'
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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14 --output '$output'
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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15 ]]></command>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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16 <inputs>
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17 <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Contigs fasta file"/>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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18 <param name="input_tabular" type="data" format="tabular" label="Tabular bedtools Genome Coverage histogram file" help="Set the bedtools Genome Coverage Output type to be Data suitable for Histogram"/>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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19 </inputs>
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20 <outputs>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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21 <data name="output" format="tabular"/>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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22 </outputs>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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23 <tests>
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24 <test expect_num_outputs="1">
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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25 <param name="input_fasta" value="input_coverage_table.fasta.gz" ftype="fasta.gz"/>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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26 <param name="input_tabular" value="input_coverage_table.tabular" ftype="tabular"/>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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27 <output name="output" file="output_coverage_table.tabular" ftype="tabular"/>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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28 </test>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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29 </tests>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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30 <help><![CDATA[
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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31 **What it does**
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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32
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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33 Accepts an assembled (and possibly cut by the Cut fasta contigs tool) fasta contigs file and a tabular coverage histogram
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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34 file (produced by the bedtools Genomve Coverage tool) and outputs a tabular coverage file for use as the input to the
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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35 CONCOCT metagenome binning tool.
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36
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37 @HELP_OVERVIEW@
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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38 ]]></help>
53f2fabb9d7d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
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39 <expand macro="citations"/>
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40 </tool>