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comparison concoct_coverage_table.xml @ 2:2b6ed3a91fbe draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
author iuc
date Thu, 07 Jul 2022 08:28:54 +0000
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children 9e924fbcbcee
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1:aff48b4c0ecc 2:2b6ed3a91fbe
1 <tool id="concoct_coverage_table" name="CONCOCT: Generate the input coverage table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>for CONCOCT</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="1.15.1">samtools</requirement>
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[
10 mkdir 'mapping' &&
11 #for $e in $bamfiles
12 ln -s '$e' 'mapping/${e.element_identifier}.sorted.bam' &&
13 samtools index 'mapping/${e.element_identifier}.sorted.bam' 'mapping/${e.element_identifier}.bam.bai' &&
14 mv 'mapping/${e.element_identifier}.sorted.bam' 'mapping/${e.element_identifier}.bam' &&
15 #end for
16 concoct_coverage_table.py
17 '$bedfile'
18 mapping/*.bam
19 > '$output'
20 ]]></command>
21 <inputs>
22 <param name="bedfile" type="data" format="bed" label="Contigs BEDFile" help="The file should have four columns representing: 'Contig ID, Start Position, End Position and SubContig ID' respectively. The Subcontig ID must contain the pattern 'concoct_part_[0-9]*' while the contigs which are not cutup cannot contain this pattern. This file can be generated by the cut_up_fasta tool."/>
23 <param name="bamfiles" type="data" format="bam" label="Sorted BAM files" multiple="true" help="BAM files with mappings to the original contigs, after sorting"/>
24 </inputs>
25 <outputs>
26 <data name="output" format="tabular"/>
27 </outputs>
28 <tests>
29 <test expect_num_outputs="1">
30 <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/>
31 <param name="bamfiles" value="ten_reads_two_contigs-s.bam" ftype="bam"/>
32 <output name="output" ftype="tabular">
33 <assert_contents>
34 <has_text text="contig-21000001.concoct_part_0"/>
35 <has_n_lines n="11"/>
36 </assert_contents>
37 </output>
38 </test>
39 </tests>
40 <help><![CDATA[
41 **What it does**
42
43 Accepts an assembled (and possibly cut by the Cut fasta contigs tool) fasta contigs file and a tabular coverage histogram
44 file (produced by the bedtools Genomve Coverage tool) and outputs a tabular coverage file for use as the input to the
45 CONCOCT metagenome binning tool.
46
47 @HELP_OVERVIEW@
48 ]]></help>
49 <expand macro="citations"/>
50 </tool>