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comparison nanopolish_extract.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 <tool id="nanopolish_extract" name="Nanopolish::extract" version="0.7.2">
2
3 <description>FAST5 to FASTQ/A extraction</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 python3 $__tool_directory__/nanopolish_extract.py $input $output \${GALAXY_SLOTS:-1}
23
24 ]]>
25 </command>
26
27 <!-- ***************************************************************** -->
28
29 <inputs>
30
31 <param name="input" type="data" format="fast5_archive" label="Input reads" />
32 <param name="out_format" type="select" label="Output format">
33 <option value="fastq" selected="true">fastq</option>
34 <option value="fasta">fasta</option>
35 </param>
36
37 </inputs>
38
39 <!-- ***************************************************************** -->
40
41 <outputs>
42
43 <data name="output" format="fastqsanger" label="${tool.name} on ${on_string}">
44 <change_format>
45 <when input="out_format" value="fasta" format="fasta" />
46 </change_format>
47 </data>
48
49 </outputs>
50
51 <!-- ***************************************************************** -->
52
53 <tests>
54 <test>
55 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
56 <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
57 </test>
58 </tests>
59
60 <!-- ***************************************************************** -->
61
62 <help>
63 <![CDATA[
64
65 **Description**
66
67 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
68 sequencing data. Nanopolish can calculate an improved consensus sequence for a
69 draft genome assembly, detect base modifications, call SNPs and indels with
70 respect to a reference genome and more.
71
72 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
73 as input, such as can be produced by `poretools combine`, and always outputs a
74 single FASTQ file.
75
76 This is the `extract` module.
77
78 ]]>
79 </help>
80
81 <!-- ***************************************************************** -->
82
83 <citations>
84 </citations>
85
86 </tool>