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comparison macros.xml @ 0:179342c7b86c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
author iuc
date Wed, 12 Oct 2022 07:43:59 +0000
parents
children 630e6aeeb7e8
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-1:000000000000 0:179342c7b86c
1 <macros>
2 <token name="@TOOL_VERSION@">1.7.2</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">21.01</token>
5 <xml name="bio_tools">
6 <xrefs>
7 <xref type="bio.tools">medaka</xref>
8 </xrefs>
9 </xml>
10 <xml name="requirements">
11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
13 <yield />
14 </requirements>
15 </xml>
16 <xml name="version_command">
17 <version_command>medaka --version</version_command>
18 </xml>
19 <xml name="citations">
20 <citations>
21 <citation type="bibtex">@online{medaka,
22 author = {Oxford Nanopore Technologies Ltd.},
23 title = {medaka},
24 year = 2020,
25 url = {https://github.com/nanoporetech/medaka},
26 urldate = {2020-05-06}
27 }</citation>
28 </citations>
29 </xml>
30
31 <!--
32 command
33 -->
34
35 <token name="@REF_FASTA@"><![CDATA[
36 #if $reference_source.reference_source_selector == 'history':
37 #if $reference_source.ref_file.ext.endswith(".gz")
38 gunzip -c '$reference_source.ref_file' > reference.fa &&
39 #else
40 ln -f -s '$reference_source.ref_file' reference.fa &&
41 #end if
42 #else:
43 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
44 #end if
45 ]]></token>
46
47 <!--
48 input
49 -->
50
51 <xml name="b" token_argument="-b">
52 <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
53 </xml>
54 <xml name="model" token_argument="-m" token_label="Select model">
55 <param argument="@ARGUMENT@" type="select" label="@LABEL@" help="For best results it is important to specify the correct model,
56 according to the basecaller used. Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION
57 or PromethION), iii) the basecaller variant, and iv) the basecaller version">
58 <option value="r103_fast_g507">r103_fast_g507</option>
59 <option value="r103_fast_snp_g507">r103_fast_snp_g507</option>
60 <option value="r103_fast_variant_g507">r103_fast_variant_g507</option>
61 <option value="r103_hac_g507">r103_hac_g507</option>
62 <option value="r103_hac_snp_g507">r103_hac_snp_g507</option>
63 <option value="r103_hac_variant_g507">r103_hac_variant_g507</option>
64 <option value="r103_min_high_g345">r103_min_high_g345</option>
65 <option value="r103_min_high_g360">r103_min_high_g360</option>
66 <option value="r103_prom_high_g360">r103_prom_high_g360</option>
67 <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
68 <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
69 <option value="r103_sup_g507">r103_sup_g507</option>
70 <option value="r103_sup_snp_g507">r103_sup_snp_g507</option>
71 <option value="r103_sup_variant_g507">r103_sup_variant_g507</option>
72 <option value="r1041_e82_400bps_fast_g615">r1041_e82_400bps_fast_g615</option>
73 <option value="r1041_e82_400bps_fast_variant_g615">r1041_e82_400bps_fast_variant_g615</option>
74 <option value="r1041_e82_400bps_hac_g615">r1041_e82_400bps_hac_g615</option>
75 <option value="r1041_e82_400bps_hac_variant_g615">r1041_e82_400bps_hac_variant_g615</option>
76 <option value="r1041_e82_400bps_sup_g615">r1041_e82_400bps_sup_g615</option>
77 <option value="r1041_e82_400bps_sup_variant_g615">r1041_e82_400bps_sup_variant_g615</option>
78 <option value="r104_e81_fast_g5015">r104_e81_fast_g5015</option>
79 <option value="r104_e81_hac_g5015">r104_e81_hac_g5015</option>
80 <option value="r104_e81_sup_g5015">r104_e81_sup_g5015</option>
81 <option value="r104_e81_fast_variant_g5015">r104_e81_fast_variant_g5015</option>
82 <option value="r104_e81_hac_variant_g5015">r104_e81_hac_variant_g5015</option>
83 <option value="r104_e81_sup_g610">r104_e81_sup_g610</option>
84 <option value="r104_e81_sup_variant_g610">r104_e81_sup_variant_g610</option>
85 <option value="r10_min_high_g303">r10_min_high_g303</option>
86 <option value="r10_min_high_g340">r10_min_high_g340</option>
87 <option value="r941_e81_fast_variant_g514">r941_e81_fast_variant_g514</option>
88 <option value="r941_e81_hac_g514">r941_e81_hac_g514</option>
89 <option value="r941_e81_hac_variant_g514">r941_e81_hac_variant_g514</option>
90 <option value="r941_e81_sup_g514">r941_e81_sup_g514</option>
91 <option value="r941_e81_sup_variant_g514">r941_e81_sup_variant_g514</option>
92 <option value="r941_min_fast_g303">r941_min_fast_g303</option>
93 <option value="r941_min_fast_g507">r941_min_fast_g507</option>
94 <option value="r941_min_fast_snp_g507">r941_min_fast_snp_g507</option>
95 <option value="r941_min_fast_variant_g507">r941_min_fast_variant_g507</option>
96 <option value="r941_min_hac_g507">r941_min_hac_g507</option>
97 <option value="r941_min_hac_snp_g507">r941_min_hac_snp_g507</option>
98 <option value="r941_min_hac_variant_g507">r941_min_hac_variant_g507</option>
99 <option value="r941_min_high_g303">r941_min_high_g303</option>
100 <option value="r941_min_high_g330">r941_min_high_g330</option>
101 <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
102 <option value="r941_min_high_g344">r941_min_high_g344</option>
103 <option value="r941_min_high_g351">r941_min_high_g351</option>
104 <option value="r941_min_high_g360" selected="true">r941_min_high_g360</option>
105 <option value="r941_min_sup_g507">r941_min_sup_g507</option>
106 <option value="r941_min_sup_snp_g507">r941_min_sup_snp_g507</option>
107 <option value="r941_min_sup_variant_g507">r941_min_sup_variant_g507</option>
108 <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
109 <option value="r941_prom_fast_g507">r941_prom_fast_g507</option>
110 <option value="r941_prom_fast_snp_g507">r941_prom_fast_snp_g507</option>
111 <option value="r941_prom_fast_variant_g507">r941_prom_fast_variant_g507</option>
112 <option value="r941_prom_hac_g507">r941_prom_hac_g507</option>
113 <option value="r941_prom_hac_snp_g507">r941_prom_hac_snp_g507</option>
114 <option value="r941_prom_hac_variant_g507">r941_prom_hac_variant_g507</option>
115 <option value="r941_prom_high_g303">r941_prom_high_g303</option>
116 <option value="r941_prom_high_g330">r941_prom_high_g330</option>
117 <option value="r941_prom_high_g344">r941_prom_high_g344</option>
118 <option value="r941_prom_high_g360">r941_prom_high_g360</option>
119 <option value="r941_prom_high_g4011">r941_prom_high_g4011</option>
120 <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
121 <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
122 <option value="r941_prom_snp_g360">r941_prom_snp_g360</option>
123 <option value="r941_prom_sup_g507">r941_prom_sup_g507</option>
124 <option value="r941_prom_sup_snp_g507">r941_prom_sup_snp_g507</option>
125 <option value="r941_prom_sup_variant_g507">r941_prom_sup_variant_g507</option>
126 <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
127 <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
128 <option value="r941_prom_variant_g360">r941_prom_variant_g360</option>
129 <option value="r941_sup_plant_g610">r941_sup_plant_g610</option>
130 <option value="r941_sup_plant_variant_g610">r941_sup_plant_variant_g610</option>
131 </param>
132 </xml>
133 <xml name="reference">
134 <conditional name="reference_source">
135 <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
136 <option value="cached">Use a built-in genome</option>
137 <option value="history">Use a genome from history</option>
138 </param>
139 <when value="cached">
140 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
141 <options from_data_table="all_fasta">
142 <filter type="sort_by" column="2"/>
143 <validator type="no_options" message="No reference genomes are available"/>
144 </options>
145 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
146 </param>
147 </when>
148 <when value="history">
149 <param name="ref_file" type="data" format="fasta,fasta.gz" 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"/>
150 </when>
151 </conditional>
152 </xml>
153
154 <!--
155 Help
156 -->
157
158 <token name="@WID@"><![CDATA[
159 *medaka* is a tool suite to create a consensus sequence from nanopore sequencing data.
160
161 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.
162 ]]></token>
163
164 <token name="@MODELS@"><![CDATA[
165
166 ----
167
168 .. class:: infomark
169
170 **Models**
171
172 For best results it is important to specify the correct model, -m in the above, according to the basecaller used. Allowed values can be found by running medaka tools list\_models.
173
174 Medaka models are named to indicate i) the pore type, ii) the sequencing device (MinION or PromethION), iii) the basecaller variant, and iv) the basecaller version, with the format:
175
176 ::
177
178 {pore}_{device}_{caller variant}_{caller version}
179
180 For example the model named r941_min_fast_g303 should be used with data from MinION (or GridION) R9.4.1 flowcells using the fast Guppy basecaller version 3.0.3. By contrast the model
181 r941_prom_hac_g303 should be used with PromethION data and the high accuracy basecaller (termed "hac" in Guppy configuration files). Where a version of Guppy has been used without an exactly corresponding medaka model, the medaka model with the highest version equal to or less than the guppy version should be selected.
182
183 ]]></token>
184
185 <token name="@REFERENCES@"><![CDATA[
186 More information are available in the `manual <https://github.com/nanoporetech/medaka/tree/master/docs>`_ and `github <https://github.com/nanoporetech/medaka>`_.
187 ]]></token>
188 </macros>