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comparison scrappie_raw.xml @ 0:30c2b84b4117 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/scrappie commit bf5788ad5a3293446a50a3246b44ba09174c9b71
author jdv
date Wed, 30 Aug 2017 02:55:35 -0400
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-1:000000000000 0:30c2b84b4117
1 <tool id="scrappie_raw" name="Scrappie (raw)" version="1.0.0">
2
3 <description>ONT development basecaller</description>
4
5 <!-- ***************************************************************** -->
6
7 <!--
8 <requirements>
9 <requirement type="package" version="1.0.0">scrappie</requirement>
10 </requirements>
11 -->
12
13 <!-- ***************************************************************** -->
14
15 <version_command>scrappie version | perl -wnE'print "$1\n" for /scrappie (.+)/g'</version_command>
16
17 <!-- ***************************************************************** -->
18
19 <command detect_errors="aggressive">
20 <![CDATA[
21
22 python3 $__tool_directory__/scrappie_raw.py $input $output \${GALAXY_SLOTS:-1}
23
24 ]]>
25 </command>
26
27 <!-- ***************************************************************** -->
28
29 <inputs>
30
31 <param name="input" type="data" format="fast5_archive" label="Input reads" />
32
33 </inputs>
34
35 <!-- ***************************************************************** -->
36
37 <outputs>
38
39 <data name="output" format="fasta" label="${tool.name} on ${on_string} (called.fasta)" />
40
41 </outputs>
42
43 <!-- ***************************************************************** -->
44
45 <tests>
46 <!-- multithreaded output is non-deterministic, so simply compare file
47 sizes -->
48 <test>
49 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
50 <output name="output" file="test_data.fasta" compare="sim_size" delta="0" />
51 </test>
52 </tests>
53
54 <!-- ***************************************************************** -->
55
56 <help>
57 <![CDATA[
58
59 **Description**
60
61 Scrappie provides recurrent neural network basecalling for Oxford Nanopore
62 MinION data. It is a technology demonstrator for the Oxford Nanopore
63 Research Algorithms group. It is designed for improved calling of
64 homopolymers over nanonet. Scrappie is provided unsupported by Oxford
65 Nanopore Technologies.
66
67 The Galaxy wrapper has modified scrappie to take a gzip tarball of FAST5 reads
68 as input, such as can be produced by `poretools combine`, and always outputs a
69 single FASTA file.
70
71 This is the raw basecaller.
72
73 ]]>
74 </help>
75
76 <!-- ***************************************************************** -->
77
78 <citations>
79 </citations>
80
81 </tool>