Mercurial > repos > iuc > medaka_consensus_pipeline

comparison macros.xml @ 0:ef94bace3a3c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"
author iuc
date Sat, 23 May 2020 13:38:26 -0400
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children 551f8c9bc4cf
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-1:000000000000 0:ef94bace3a3c
1 <?xml version="1.0"?>
2 <macros>
3 <token name="@TOOL_VERSION@">1.0.1</token>
4 <token name="@PROFILE@">18.01</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
8 </requirements>
9 </xml>
10 <xml name="version_command">
11 <version_command>medaka --version</version_command>
12 </xml>
13 <xml name="citations">
14 <citations>
15 <citation type="bibtex">@online{medaka,
16 author = {Oxford Nanopore Technologies Ltd.},
17 title = {medaka},
18 year = 2020,
19 url = {https://github.com/nanoporetech/medaka},
20 urldate = {2020-05-06}
21 }</citation>
22 </citations>
23 </xml>
24
25 <!--
26 command
27 -->
28
29 <token name="@REF_FASTA@"><![CDATA[
30 #if $reference_source.reference_source_selector == 'history':
31 ln -f -s '$reference_source.ref_file' 'reference.fa' &&
32 #else:
33 ln -f -s '$reference_source.ref_file.fields.path' 'reference.fa' &&
34 #end if
35 ]]></token>
36
37 <!--
38 input
39 -->
40
41 <xml name="b" token_argument="-b">
42 <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
43 </xml>
44 <xml name="model" token_argument="-m" token_label="Select model">
45 <param argument="@ARGUMENT@" type="select" label="@LABEL@">
46 <option value="r10_min_high_g303">r10_min_high_g303</option>
47 <option value="r10_min_high_g340">r10_min_high_g340</option>
48 <option value="r103_min_high_g345">r103_min_high_g345</option>
49 <option value="r103_min_high_g360">r103_min_high_g360</option>
50 <option value="r103_prom_high_g360">r103_prom_high_g360</option>
51 <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
52 <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
53 <option value="r941_min_fast_g303">r941_min_fast_g303</option>
54 <option value="r941_min_high_g303">r941_min_high_g303</option>
55 <option value="r941_min_high_g330">r941_min_high_g330</option>
56 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
57 <option value="r941_min_high_g344">r941_min_high_g344</option>
58 <option value="r941_min_high_g351" selected="true">r941_min_high_g351</option>
59 <option value="r941_min_high_g360">r941_min_high_g360</option>
60 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
61 <option value="r941_prom_high_g303">r941_prom_high_g303</option>
62 <option value="r941_prom_high_g330">r941_prom_high_g330</option>
63 <option value="r941_prom_high_g344">r941_prom_high_g344</option>
64 <option value="r941_prom_high_g360">r941_prom_high_g360</option>
65 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
66 <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
67 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
68 <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
69 </param>
70 </xml>
71 <xml name="reference">
72 <conditional name="reference_source">
73 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
74 <option value="cached">Use a built-in genome</option>
75 <option value="history">Use a genome from history</option>
76 </param>
77 <when value="cached">
78 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
79 <options from_data_table="all_fasta">
80 <filter type="sort_by" column="2" />
81 <validator type="no_options" message="No reference genomes are available" />
82 </options>
83 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
84 </param>
85 </when>
86 <when value="history">
87 <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
88 </when>
89 </conditional>
90 </xml>
91
92 <!--
93 Help
94 -->
95
96 <token name="@WID@"><![CDATA[
97 medaka is a tool suite to create a consensus sequence from nanopore sequencing data.
98
99 This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.
100 ]]></token>
101 <token name="@REFERENCES@"><![CDATA[
102 More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_.
103 ]]></token>
104 </macros>