Mercurial > repos > iuc > medaka_consensus

annotate medaka.xml @ 0:1c4402b9244d draft

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