Mercurial > repos > iuc > medaka_snp
comparison macros.xml @ 0:179342c7b86c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
author | iuc |
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date | Wed, 12 Oct 2022 07:43:59 +0000 |
parents | |
children | 630e6aeeb7e8 |
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-1:000000000000 | 0:179342c7b86c |
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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> |