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comparison albacore_1D.xml @ 0:f8e25d69167d draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/albacore commit bf5788ad5a3293446a50a3246b44ba09174c9b71
author jdv
date Wed, 30 Aug 2017 02:47:27 -0400
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1 <tool id="albacore_1D" name="Albacore 1D" version="1.2.6">
2
3 <description>ONT production basecaller</description>
4
5 <!-- ***************************************************************** -->
6
7 <!--
8 <requirements>
9 <requirement type="package" version="1.2.6">albacore</requirement>
10 </requirements>
11 -->
12
13 <!-- ***************************************************************** -->
14
15 <version_command>read_fast5_basecaller.py --version | perl -wnE'print "$1\n" for /\(version ([^\)]+)\)/g'</version_command>
16
17 <!-- ***************************************************************** -->
18
19 <command detect_errors="aggressive">
20 <![CDATA[
21
22 python3 $__tool_directory__/albacore_1D.py $input $output \${GALAXY_SLOTS:-1}
23
24 ]]>
25 </command>
26
27 <!-- ***************************************************************** -->
28
29 <inputs>
30
31 <param name="input" type="data" format="fast5_archive" label="Input reads" />
32
33 </inputs>
34
35 <!-- ***************************************************************** -->
36
37 <outputs>
38
39 <data name="output" format="fastq" label="${tool.name} on ${on_string} (called.fastq)" />
40
41 </outputs>
42
43 <!-- ***************************************************************** -->
44
45 <tests>
46 <test>
47 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
48 <output name="output" file="test_data.fastq" compare="diff" />
49 </test>
50 </tests>
51
52 <!-- ***************************************************************** -->
53
54 <help>
55 <![CDATA[
56
57 **Description**
58
59 Albacore is a tool for basecalling Oxford Nanopore reads. It is distributed by
60 ONT to authorized community members only and thus is not packaged through
61 Galaxy or Bioconda. End users are responsible for installing and testing the
62 albacore software themselves and ensuring that it is in the galaxy user $PATH.
63
64 The Galaxy wrapper has modified albacore to take a gzip tarball of FAST5 reads
65 as input, such as can be produced by `poretools combine`, and always outputs a
66 single FASTQ file.
67
68 This is the 1D basecaller.
69
70 ]]>
71 </help>
72
73 <!-- ***************************************************************** -->
74
75 <citations>
76 </citations>
77
78 </tool>