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comparison canu.xml @ 0:7d87a6450883 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/canu commit b1d1a13639aff19178a1b521a476a179c39948cc-dirty
author jdv
date Wed, 06 Sep 2017 12:24:44 -0400
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-1:000000000000 0:7d87a6450883
1 <tool id="canu" name="Canu" version="1.6">
2
3 <description>Assembler optimized for long error-prone reads</description>
4
5 <!-- ***************************************************************** -->
6
7 <!--
8 <requirements>
9 <requirement type="package" version="1.6">canu</requirement>
10 </requirements>
11 -->
12
13 <!-- ***************************************************************** -->
14
15 <version_command>canu --version | perl -wnE'print "$1\n" for /^Canu (?:snapshot v)?(\S+)/g'</version_command>
16
17
18 <!-- ***************************************************************** -->
19
20 <command detect_errors="aggressive">
21 <![CDATA[
22
23 canu
24
25 -p canu_galaxy
26 -d out_dir
27 useGrid=false
28 genomeSize=$genome_size
29 rawErrorRate=$raw_error_rate
30 correctedErrorRate=$corrected_error_rate
31 minReadLength=$min_read_length
32 minOverlapLength=$min_overlap
33 minThreads=\${GALAXY_SLOTS:-1}
34 maxThreads=\${GALAXY_SLOTS:-1}
35 gnuplotTested=true
36 useGrid=false
37 $mode
38 $input
39
40
41 ]]>
42 </command>
43
44 <!-- ***************************************************************** -->
45
46 <inputs>
47
48 <param name="input" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Input reads" />
49 <param name="mode" type="select">
50 <option value="-nanopore-raw" selected="true">nanopore raw</option>
51 <option value="-pacbio-raw">pacbio raw</option>
52 <option value="-nanopore-corrected">nanopore corrected</option>
53 <option value="-pacbio-corrected">pacbio corrected</option>
54 </param>
55 <param name="genome_size" type="text" size="5" label="Estimated genome size (e.g. 80m, 15k, 2g)" />
56 <param name="raw_error_rate" type="float" value="0.500" min="0" max="1" size="5" label="Maximum raw overlap mismatch (0-1)" />
57 <param name="corrected_error_rate" type="float" value="0.144" min="0" max="1" size="5" label="Maximum corrected overlap mismatch (0-1)" />
58 <param name="min_read_length" type="integer" value="1000" min="1" size="5" label="Minimum read length" />
59 <param name="min_overlap" type="integer" value="500" min="1" size="5" label="Minimum overlap" />
60
61 </inputs>
62
63 <!-- ***************************************************************** -->
64
65 <outputs>
66
67 <data name="contigs" format="fasta" from_work_dir="out_dir/canu_galaxy.contigs.fasta" label="${tool.name} on ${on_string} (contigs)" />
68 <data name="unitigs" format="fasta" from_work_dir="out_dir/canu_galaxy.unitigs.fasta" label="${tool.name} on ${on_string} (unitigs)" />
69
70 </outputs>
71
72 <!-- ***************************************************************** -->
73
74 <!--
75 <tests>
76 <test>
77 <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
78 <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
79 </test>
80 </tests>
81 -->
82
83 <!-- ***************************************************************** -->
84
85 <help>
86 <![CDATA[
87
88 **Description**
89
90 Nanopolish is a software package for signal-level analysis of Oxford Nanopore
91 sequencing data. Nanopolish can calculate an improved consensus sequence for a
92 draft genome assembly, detect base modifications, call SNPs and indels with
93 respect to a reference genome and more.
94
95 The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
96 as input, such as can be produced by `poretools combine`, and always outputs a
97 single FASTQ file.
98
99 This is the `extract` module.
100
101 ]]>
102 </help>
103
104 <!-- ***************************************************************** -->
105
106 <citations>
107 </citations>
108
109 </tool>