annotate concoct_coverage_table.xml @ 4:0442e7102125 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 6bcf71ac8fae2a84117069dc00b3c4cac6d20fa5

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     <command detect_errors="exit_code"><![CDATA[
8 #import re
9 mkdir 'mapping' &&
10 #if $mode.type == 'individual'
11     #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.bamfile))
12 ln -s '$mode.bamfile' 'mapping/${identifier}.sorted.bam' &&
13 samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
14 mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
15 #else
16     #for $e in $mode.bamfiles
17         #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
18 ln -s '$e' 'mapping/${identifier}.sorted.bam' &&
19 samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
20 mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
21     #end for
22 #end if
23 concoct_coverage_table.py
24     '$bedfile'
25     mapping/*.bam
26     > '$output'
27     ]]></command>
28     <inputs>
29         <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 CONCOCT: Cut up contigs tool."/>
30         <conditional name="mode">
31             <param name="type" type="select" label="Type of assembly used to generate the contigs" help="Information used to process the BAM files">
32                 <option value="individual">Individual assembly: 1 run per BAM file</option>
33                 <option value="co">Co-assembly: all BAM files processed together</option>
34             </param>
35             <when value="individual">
36                 <param name="bamfile" type="data" format="bam" label="Sorted BAM file" help="BAM file with mappings to the original contigs, after sorting"/>
37             </when>
38             <when value="co">
39                 <param name="bamfiles" type="data" format="bam" label="Sorted BAM files" multiple="true" help="BAM files with mappings to the original contigs, after sorting"/>
40             </when>
41         </conditional>
42     </inputs>
43     <outputs>
44         <data name="output" format="tabular"/>
45     </outputs>
46     <tests>
47         <test expect_num_outputs="1">
48             <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/>
49             <conditional name="mode">
50                 <param name="type" value="individual"/>
51                 <param name="bamfile" value="ten_reads_two_contigs-s.bam" ftype="bam"/>
52             </conditional>
53             <output name="output" ftype="tabular">
54                 <assert_contents>
55                     <has_text text="contig-21000001.concoct_part_0"/>
56                     <has_n_lines n="11"/>
57                 </assert_contents>
58             </output>
59         </test>
60         <test expect_num_outputs="1">
61             <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/>
62             <conditional name="mode">
63                 <param name="type" value="co"/>
64                 <param name="bamfiles" value="ten_reads_two_contigs-s.bam,ten_reads_two_contigs-s_2.bam" ftype="bam"/>
65             </conditional>
66             <output name="output" ftype="tabular">
67                 <assert_contents>
68                     <has_text text="cov_mean_sample_ten_reads_two_contigs-s.bam"/>
69                     <has_text text="cov_mean_sample_ten_reads_two_contigs-s_2.bam"/>
70                     <has_text text="contig-21000001.concoct_part_0"/>
71                     <has_n_lines n="11"/>
72                 </assert_contents>
73             </output>
74         </test>
75     </tests>
76     <help><![CDATA[
77 **What it does**
78 
79 Accepts an assembled (and possibly cut by the Cut fasta contigs tool) fasta contigs file and a tabular coverage histogram
80 file (produced by the bedtools Genomve Coverage tool) and outputs a tabular coverage file for use as the input to the
81 CONCOCT metagenome binning tool.
82 
83 @HELP_OVERVIEW@
84     ]]></help>
85     <expand macro="citations"/>
86 </tool>