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comparison nanopolish_index.xml @ 7:32cb27adeb34 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanopolish commit 2dabc22c3707cc87100b094b25705160b842e9f9-dirty
author jdv
date Mon, 12 Feb 2018 00:58:10 -0500
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6:36cc4ae4160e 7:32cb27adeb34
1 <tool id="nanopolish_index" name="Nanopolish::index" version="0.8.5">
2
3 <description>Index FASTQ reads in FAST5 file</description>
4
5 <!-- ***************************************************************** -->
6
7 <requirements>
8 <requirement type="package" version="0.8.5">nanopolish</requirement>
9 </requirements>
10
11 <!-- ***************************************************************** -->
12
13 <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
14
15 <!-- ***************************************************************** -->
16
17 <command detect_errors="aggressive">
18 <![CDATA[
19
20 perl $__tool_directory__/nanopolish_index.pl
21
22 --reads $input_reads
23 --fast5 $input_fast5
24 --out $out_index
25
26 ]]>
27 </command>
28
29 <!-- ***************************************************************** -->
30
31 <inputs>
32
33 <param name="input_reads" type="data" format="fasta,fastq" label="Input reads (FASTA/Q)" />
34 <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" />
35
36 </inputs>
37
38 <!-- ***************************************************************** -->
39
40 <outputs>
41
42 <data name="out_index" format="tar" label="${tool.name} on ${on_string}" />
43
44 </outputs>
45
46 <!-- ***************************************************************** -->
47
48 <tests>
49 <test>
50 <param name="input_reads" value="called.fa" ftype="fasta" />
51 <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
52 <output name="out_index" file="index.tar" compare="sim_size" delta="100"/>
53 </test>
54 </tests>
55
56 <!-- ***************************************************************** -->
57
58 <help>
59 <![CDATA[
60
61 **Description**
62
63 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
64 sequencing data. Nanopolish can calculate an improved consensus sequence for a
65 draft genome assembly, detect base modifications, call SNPs and indels with
66 respect to a reference genome and more.
67
68 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
69 as input, such as can be produced by `poretools combine`, and always outputs a
70 single FASTQ file.
71
72 This is the `index` module.
73
74 ]]>
75 </help>
76
77 <!-- ***************************************************************** -->
78
79 <citations>
80 </citations>
81
82 </tool>