Mercurial > repos > iuc > concoct_coverage_table

comparison coverage_table.xml @ 0:53f2fabb9d7d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
author iuc
date Sun, 13 Mar 2022 08:42:29 +0000
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1 <tool id="concoct_coverage_table" name="CONCOCT coverage table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description></description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[
8 python '$__tool_directory__/coverage_table.py'
9 --input_fasta '$input_fasta'
10 #if $input_fasta.is_of_type('fasta.gz'):
11 --gzipped
12 #end if
13 --input_tabular '$input_tabular'
14 --output '$output'
15 ]]></command>
16 <inputs>
17 <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Contigs fasta file"/>
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"/>
19 </inputs>
20 <outputs>
21 <data name="output" format="tabular"/>
22 </outputs>
23 <tests>
24 <test expect_num_outputs="1">
25 <param name="input_fasta" value="input_coverage_table.fasta.gz" ftype="fasta.gz"/>
26 <param name="input_tabular" value="input_coverage_table.tabular" ftype="tabular"/>
27 <output name="output" file="output_coverage_table.tabular" ftype="tabular"/>
28 </test>
29 </tests>
30 <help><![CDATA[
31 **What it does**
32
33 Accepts an assembled (and possibly cut by the Cut fasta contigs tool) fasta contigs file and a tabular coverage histogram
34 file (produced by the bedtools Genomve Coverage tool) and outputs a tabular coverage file for use as the input to the
35 CONCOCT metagenome binning tool.
36
37 @HELP_OVERVIEW@
38 ]]></help>
39 <expand macro="citations"/>
40 </tool>