Mercurial > repos > iuc > concoct_coverage_table
comparison coverage_table.xml @ 0:7e01297a3b4a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 40a09cbfd6052f7b0295946621db1bdf58228b09"
| author | iuc |
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| date | Sun, 13 Mar 2022 08:45:32 +0000 |
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| children |
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| -1:000000000000 | 0:7e01297a3b4a |
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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> |