Mercurial > repos > iuc > concoct_coverage_table

annotate concoct_coverage_table.xml @ 5:fd31cd168efc draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 86e1afebec29c10ef1e31196b23c24fde2d086da
author iuc
date Sun, 12 Nov 2023 14:31:03 +0000
parents 5ded3318cf8a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
1 <tool id="concoct_coverage_table" name="CONCOCT: Generate the input coverage table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
2 <description>for CONCOCT</description>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
3 <macros>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
5 </macros>
5
fd31cd168efc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 86e1afebec29c10ef1e31196b23c24fde2d086da
iuc
parents: 3
diff changeset
6 <expand macro="biotools"/>
3
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
7 <expand macro="requirements"/>
2
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
3
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
9 #import re
2
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
10 mkdir 'mapping' &&
3
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
11 #if $mode.type == 'individual'
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
12 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.bamfile))
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
13 ln -s '$mode.bamfile' 'mapping/${identifier}.sorted.bam' &&
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
14 samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
15 mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
16 #else
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
17 #for $e in $mode.bamfiles
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
18 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
19 ln -s '$e' 'mapping/${identifier}.sorted.bam' &&
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
20 samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
21 mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
22 #end for
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
23 #end if
2
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
24 concoct_coverage_table.py
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
25 '$bedfile'
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
26 mapping/*.bam
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
27 > '$output'
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
28 ]]></command>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
29 <inputs>
3
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
30 <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."/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
31 <conditional name="mode">
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
32 <param name="type" type="select" label="Type of assembly used to generate the contigs" help="Information used to process the BAM files">
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
33 <option value="individual">Individual assembly: 1 run per BAM file</option>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
34 <option value="co">Co-assembly: all BAM files processed together</option>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
35 </param>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
36 <when value="individual">
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
37 <param name="bamfile" type="data" format="bam" label="Sorted BAM file" help="BAM file with mappings to the original contigs, after sorting"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
38 </when>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
39 <when value="co">
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
40 <param name="bamfiles" type="data" format="bam" label="Sorted BAM files" multiple="true" help="BAM files with mappings to the original contigs, after sorting"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
41 </when>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
42 </conditional>
2
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
43 </inputs>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
44 <outputs>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
45 <data name="output" format="tabular"/>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
46 </outputs>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
47 <tests>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
48 <test expect_num_outputs="1">
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
49 <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/>
3
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
50 <conditional name="mode">
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
51 <param name="type" value="individual"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
52 <param name="bamfile" value="ten_reads_two_contigs-s.bam" ftype="bam"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
53 </conditional>
2
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
54 <output name="output" ftype="tabular">
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
55 <assert_contents>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
56 <has_text text="contig-21000001.concoct_part_0"/>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
57 <has_n_lines n="11"/>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
58 </assert_contents>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
59 </output>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
60 </test>
3
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
61 <test expect_num_outputs="1">
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
62 <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
63 <conditional name="mode">
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
64 <param name="type" value="co"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
65 <param name="bamfiles" value="ten_reads_two_contigs-s.bam,ten_reads_two_contigs-s_2.bam" ftype="bam"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
66 </conditional>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
67 <output name="output" ftype="tabular">
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
68 <assert_contents>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
69 <has_text text="cov_mean_sample_ten_reads_two_contigs-s.bam"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
70 <has_text text="cov_mean_sample_ten_reads_two_contigs-s_2.bam"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
71 <has_text text="contig-21000001.concoct_part_0"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
72 <has_n_lines n="11"/>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
73 </assert_contents>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
74 </output>
5ded3318cf8a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
iuc
parents: 2
diff changeset
75 </test>
2
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
76 </tests>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
77 <help><![CDATA[
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
78 **What it does**
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
79
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
80 Accepts an assembled (and possibly cut by the Cut fasta contigs tool) fasta contigs file and a tabular coverage histogram
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
81 file (produced by the bedtools Genomve Coverage tool) and outputs a tabular coverage file for use as the input to the
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
82 CONCOCT metagenome binning tool.
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
83
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
84 @HELP_OVERVIEW@
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
85 ]]></help>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
86 <expand macro="citations"/>
6302656ed45d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 1a79c139165648b969d82530784cea3fc8f2d2c0"
iuc
parents:
diff changeset
87 </tool>