Mercurial > repos > iuc > medaka_consensus

comparison medaka.xml @ 0:1c4402b9244d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 28167363fc58681984e067445dd9c6a25fd33a6c"
author iuc
date Sun, 23 Feb 2020 09:04:41 -0500
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-1:000000000000 0:1c4402b9244d
1 <tool id="medaka_consensus" name="medaka_consensus" version="@VERSION@" profile="19.01">
2 <description> creates a consensus sequence from nanopore sequencing data</description>
3 <macros>
4 <token name="@VERSION@">0.11.5</token>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@VERSION@">medaka</requirement>
8 </requirements>
9 <version_command>medaka --version</version_command>
10 <command detect_errors="exit_code"><![CDATA[
11 medaka_consensus
12 -i '${basecalled}'
13 -d '${draft}'
14 -o out_dir
15 -t \${GALAXY_SLOTS:-4}
16 -m '${model}' > log.txt
17 ]]> </command>
18
19 <inputs>
20 <param name="basecalled" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz"
21 label="Basecalled data"/>
22 <param name="draft" type="data" format="fasta,fasta.gz" label="Draft assemblies"
23 help="The input assembly should be preprocessed with racon"/>
24 <param name="model" type="select" label="Model">
25 <option value="r941_min_fast_g303">r941_min_fast_g303</option>
26 <option value="r941_min_high_g303" selected="True">r941_min_high_g303</option>
27 <option value="r941_min_high_g330">r941_min_high_g330</option>
28 <option value="r941_min_high_g344">r941_min_high_g344</option>
29 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
30 <option value="r941_prom_high_g303">r941_prom_high_g303</option>
31 <option value="r941_prom_high_g344">r941_prom_high_g344</option>
32 <option value="r941_prom_high_g330">r941_prom_high_g330</option>
33 <option value="r10_min_high_g303">r10_min_high_g303</option>
34 <option value="r10_min_high_g340">r10_min_high_g340</option>
35 <option value="r103_min_high_g345">r103_min_high_g345</option>
36 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
37 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
38 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
39 </param>
40 </inputs>
41 <outputs>
42 <!-- <collection name="list_output" type="list" label="Output">
43 <discover_datasets pattern="__name_and_ext__" directory="out_dir"/>
44 </collection> -->
45 <data name="consensus" format="fasta" label="${tool.name} on ${on_string}: consensus" from_work_dir="out_dir/consensus.fasta"/>
46 <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"/>
47 </outputs>
48 <tests>
49 <test>
50 <param name="draft" value="plasmid.fasta" />
51 <param name="basecalled" value="reads.fastq" />
52 <param name="model" value="r941_min_fast_g303"/>
53 <output name="consensus" file="medaka/consensus.fasta" ftype="fasta" />
54 </test>
55 </tests>
56 <help><![CDATA[
57
58 .. class:: infomark
59
60 **What it does**
61
62 medaka is a tool to create a consensus sequence from nanopore sequencing data.
63 This task is performed using neural networks applied from a pileup of individual sequencing
64 reads against a draft assembly. It outperforms graph-based methods operating on basecalled data,
65 and can be competitive with state-of-the-art signal-based methods, whilst being much faster.
66
67
68 ]]></help>
69 </tool>