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comparison nanopolish_variants.xml @ 0:2136c2725fc4 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 0206b7bd377b39ad28592b0a02588f40575efd3e-dirty
author jdv
date Wed, 06 Sep 2017 12:15:45 -0400
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-1:000000000000 0:2136c2725fc4
1 <tool id="nanopolish_variants" name="Nanopolish::variants" version="0.7.2">
2
3 <description>Re-call consensus and variants from raw signal</description>
4
5 <!-- ***************************************************************** -->
6
7 <!--
8 <requirements>
9 <requirement type="package" version="0.7.2">nanopolish</requirement>
10 </requirements>
11 -->
12
13 <!-- ***************************************************************** -->
14
15 <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
16
17 <!-- ***************************************************************** -->
18
19 <command detect_errors="aggressive">
20 <![CDATA[
21
22 ln -s $input_bam 'input.bam' &&
23 ln -s $input_bam.metadata.bam_index input.bai &&
24
25 perl $__tool_directory__/nanopolish_variants.pl variants
26
27 --reads $input_reads
28 --bam input.bam
29 --genome $input_ref
30 --consensus $out_consensus
31 --outfile $out_variants
32 --threads \${GALAXY_SLOTS:-1}
33 --max-round $max_rounds
34 --max-haplotypes $max_haplotypes
35 --min-candidate-depth $min_candidate_depth
36 --min-candidate-frequency $min_candidate_frequency
37 --fast5 $input_fast5
38 $fix_homopolymers
39 $calculate_all_support
40
41 ]]>
42 </command>
43
44 <!-- ***************************************************************** -->
45
46 <inputs>
47
48 <param name="input_reads" type="data" format="fasta" label="Input reads (FASTA)" />
49 <param name="input_fast5" type="data" format="fast5_archive" label="Input reads (FAST5)" />
50 <param name="input_bam" type="data" format="bam" label="Alignment" />
51 <param name="input_ref" type="data" format="fasta" label="Reference" />
52 <param name="min_candidate_frequency" type="float" value="0.2" size="5" label="Minimum candidate frequency" />
53 <param name="min_candidate_depth" type="integer" min="1" value="20" size="5" label="Minimum candidate depth" />
54 <param name="max_haplotypes" type="integer" min="0" value="1000" size="5" label="Maximum haplotype combinations" />
55 <param name="max_rounds" type="integer" min="0" value="50" size="5" label="Maximum iterations" />
56 <param name="fix_homopolymers" type="boolean" checked="false" truevalue="--fix-homopolymers" falsevalue="" label="Fix homopolymers" />
57 <param name="calculate_all_support" type="boolean" checked="false" truevalue="--calculate-all-support" falsevalue="" label="Calculate support for all four bases" />
58 </inputs>
59
60 <!-- ***************************************************************** -->
61
62 <outputs>
63
64 <data name="out_variants" format="vcf" label="${tool.name} on ${on_string} (variants)" />
65 <data name="out_consensus" format="fasta" label="${tool.name} on ${on_string} (consensus)" />
66
67 </outputs>
68
69 <!-- ***************************************************************** -->
70
71 <tests>
72 </tests>
73
74 <!-- ***************************************************************** -->
75
76 <help>
77 <![CDATA[
78
79 **Description**
80
81 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
82 sequencing data. Nanopolish can calculate an improved consensus sequence for a
83 draft genome assembly, detect base modifications, call SNPs and indels with
84 respect to a reference genome and more.
85
86 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
87 as input, such as can be produced by `poretools combine`, and always outputs a
88 single FASTQ file.
89
90 This is the `extract` module.
91
92 ]]>
93 </help>
94
95 <!-- ***************************************************************** -->
96
97 <citations>
98 </citations>
99
100 </tool>