Mercurial > repos > iuc > medaka_consensus_pipeline

comparison macros.xml @ 17:d9b6a4615626 draft default tip

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/main/tools/medaka commit 450d1acaa1feae57e288d7cefb5a20cfca025fe4
author iuc
date Tue, 28 Oct 2025 09:58:19 +0000
parents fc8804320156
children
comparison
equal deleted inserted replaced
16:fc8804320156 17:d9b6a4615626
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.7.2</token> 2 <token name="@TOOL_VERSION@">2.1.1</token>
3 <token name="@VERSION_SUFFIX@">1</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">21.01</token> 4 <token name="@PROFILE@">21.01</token>
5 <xml name="bio_tools"> 5 <xml name="bio_tools">
6 <xrefs> 6 <xrefs>
7 <xref type="bio.tools">medaka</xref> 7 <xref type="bio.tools">medaka</xref>
8 </xrefs> 8 </xrefs>
9 </xml> 9 </xml>
10 <xml name="requirements"> 10 <xml name="requirements">
11 <requirements> 11 <requirements>
12 <requirement type="package" version="@TOOL_VERSION@">medaka</requirement> 12 <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
13 <requirement type="package" version="1.16.2">scipy</requirement>
13 <yield /> 14 <yield />
14 </requirements> 15 </requirements>
15 </xml> 16 </xml>
16 <xml name="version_command"> 17 <xml name="version_command">
17 <version_command>medaka --version</version_command> 18 <version_command>medaka --version</version_command>
50 51
51 <xml name="b" token_argument="-b"> 52 <xml name="b" token_argument="-b">
52 <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/> 53 <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
53 </xml> 54 </xml>
54 <xml name="model" token_argument="-m" token_label="Select model"> 55 <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 <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 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 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_g507">r103_fast_g507</option>
59 <option value="r103_fast_snp_g507">r103_fast_snp_g507</option> 60 <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_fast_variant_g507">r103_fast_variant_g507</option>
61 <option value="r103_hac_g507">r103_hac_g507</option> 62 <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_snp_g507">r103_hac_snp_g507</option>
63 <option value="r103_hac_variant_g507">r103_hac_variant_g507</option> 64 <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> 65 <option value="r103_sup_g507">r103_sup_g507</option>
70 <option value="r103_sup_snp_g507">r103_sup_snp_g507</option> 66 <option value="r103_sup_snp_g507">r103_sup_snp_g507</option>
71 <option value="r103_sup_variant_g507">r103_sup_variant_g507</option> 67 <option value="r103_sup_variant_g507">r103_sup_variant_g507</option>
68 <option value="r1041_e82_260bps_fast_g632">r1041_e82_260bps_fast_g632</option>
69 <option value="r1041_e82_260bps_fast_variant_g632">r1041_e82_260bps_fast_variant_g632</option>
70 <option value="r1041_e82_260bps_hac_g632">r1041_e82_260bps_hac_g632</option>
71 <option value="r1041_e82_260bps_hac_v4.0.0">r1041_e82_260bps_hac_v4.0.0</option>
72 <option value="r1041_e82_260bps_hac_v4.1.0">r1041_e82_260bps_hac_v4.1.0</option>
73 <option value="r1041_e82_260bps_hac_variant_g632">r1041_e82_260bps_hac_variant_g632</option>
74 <option value="r1041_e82_260bps_hac_variant_v4.1.0">r1041_e82_260bps_hac_variant_v4.1.0</option>
75 <option value="r1041_e82_260bps_joint_apk_ulk_v5.0.0">r1041_e82_260bps_joint_apk_ulk_v5.0.0</option>
76 <option value="r1041_e82_260bps_sup_g632">r1041_e82_260bps_sup_g632</option>
77 <option value="r1041_e82_260bps_sup_v4.0.0">r1041_e82_260bps_sup_v4.0.0</option>
78 <option value="r1041_e82_260bps_sup_v4.1.0">r1041_e82_260bps_sup_v4.1.0</option>
79 <option value="r1041_e82_260bps_sup_variant_g632">r1041_e82_260bps_sup_variant_g632</option>
80 <option value="r1041_e82_260bps_sup_variant_v4.1.0">r1041_e82_260bps_sup_variant_v4.1.0</option>
81 <option value="r1041_e82_400bps_bacterial_methylation">r1041_e82_400bps_bacterial_methylation</option>
72 <option value="r1041_e82_400bps_fast_g615">r1041_e82_400bps_fast_g615</option> 82 <option value="r1041_e82_400bps_fast_g615">r1041_e82_400bps_fast_g615</option>
83 <option value="r1041_e82_400bps_fast_g632">r1041_e82_400bps_fast_g632</option>
73 <option value="r1041_e82_400bps_fast_variant_g615">r1041_e82_400bps_fast_variant_g615</option> 84 <option value="r1041_e82_400bps_fast_variant_g615">r1041_e82_400bps_fast_variant_g615</option>
85 <option value="r1041_e82_400bps_fast_variant_g632">r1041_e82_400bps_fast_variant_g632</option>
74 <option value="r1041_e82_400bps_hac_g615">r1041_e82_400bps_hac_g615</option> 86 <option value="r1041_e82_400bps_hac_g615">r1041_e82_400bps_hac_g615</option>
87 <option value="r1041_e82_400bps_hac_g632">r1041_e82_400bps_hac_g632</option>
88 <option value="r1041_e82_400bps_hac_v4.0.0">r1041_e82_400bps_hac_v4.0.0</option>
89 <option value="r1041_e82_400bps_hac_v4.1.0">r1041_e82_400bps_hac_v4.1.0</option>
90 <option value="r1041_e82_400bps_hac_v4.2.0">r1041_e82_400bps_hac_v4.2.0</option>
91 <option value="r1041_e82_400bps_hac_v4.3.0">r1041_e82_400bps_hac_v4.3.0</option>
92 <option value="r1041_e82_400bps_hac_v5.0.0">r1041_e82_400bps_hac_v5.0.0</option>
93 <option value="r1041_e82_400bps_hac_v5.0.0_rl_lstm384_dwells">r1041_e82_400bps_hac_v5.0.0_rl_lstm384_dwells</option>
94 <option value="r1041_e82_400bps_hac_v5.0.0_rl_lstm384_no_dwells">r1041_e82_400bps_hac_v5.0.0_rl_lstm384_no_dwells</option>
95 <option value="r1041_e82_400bps_hac_v5.2.0">r1041_e82_400bps_hac_v5.2.0</option>
96 <option value="r1041_e82_400bps_hac_v5.2.0_rl_lstm384_dwells">r1041_e82_400bps_hac_v5.2.0_rl_lstm384_dwells</option>
97 <option value="r1041_e82_400bps_hac_v5.2.0_rl_lstm384_no_dwells">r1041_e82_400bps_hac_v5.2.0_rl_lstm384_no_dwells</option>
75 <option value="r1041_e82_400bps_hac_variant_g615">r1041_e82_400bps_hac_variant_g615</option> 98 <option value="r1041_e82_400bps_hac_variant_g615">r1041_e82_400bps_hac_variant_g615</option>
99 <option value="r1041_e82_400bps_hac_variant_g632">r1041_e82_400bps_hac_variant_g632</option>
100 <option value="r1041_e82_400bps_hac_variant_v4.1.0">r1041_e82_400bps_hac_variant_v4.1.0</option>
101 <option value="r1041_e82_400bps_hac_variant_v4.2.0">r1041_e82_400bps_hac_variant_v4.2.0</option>
102 <option value="r1041_e82_400bps_hac_variant_v4.3.0">r1041_e82_400bps_hac_variant_v4.3.0</option>
103 <option value="r1041_e82_400bps_hac_variant_v5.0.0">r1041_e82_400bps_hac_variant_v5.0.0</option>
76 <option value="r1041_e82_400bps_sup_g615">r1041_e82_400bps_sup_g615</option> 104 <option value="r1041_e82_400bps_sup_g615">r1041_e82_400bps_sup_g615</option>
105 <option value="r1041_e82_400bps_sup_v4.0.0">r1041_e82_400bps_sup_v4.0.0</option>
106 <option value="r1041_e82_400bps_sup_v4.1.0">r1041_e82_400bps_sup_v4.1.0</option>
107 <option value="r1041_e82_400bps_sup_v4.2.0">r1041_e82_400bps_sup_v4.2.0</option>
108 <option value="r1041_e82_400bps_sup_v4.3.0">r1041_e82_400bps_sup_v4.3.0</option>
109 <option value="r1041_e82_400bps_sup_v5.0.0">r1041_e82_400bps_sup_v5.0.0</option>
110 <option value="r1041_e82_400bps_sup_v5.0.0_rl_lstm384_dwells">r1041_e82_400bps_sup_v5.0.0_rl_lstm384_dwells</option>
111 <option value="r1041_e82_400bps_sup_v5.0.0_rl_lstm384_no_dwells">r1041_e82_400bps_sup_v5.0.0_rl_lstm384_no_dwells</option>
112 <option value="r1041_e82_400bps_sup_v5.2.0">r1041_e82_400bps_sup_v5.2.0</option>
113 <option value="r1041_e82_400bps_sup_v5.2.0_rl_lstm384_dwells">r1041_e82_400bps_sup_v5.2.0_rl_lstm384_dwells</option>
114 <option value="r1041_e82_400bps_sup_v5.2.0_rl_lstm384_no_dwells">r1041_e82_400bps_sup_v5.2.0_rl_lstm384_no_dwells</option>
77 <option value="r1041_e82_400bps_sup_variant_g615">r1041_e82_400bps_sup_variant_g615</option> 115 <option value="r1041_e82_400bps_sup_variant_g615">r1041_e82_400bps_sup_variant_g615</option>
116 <option value="r1041_e82_400bps_sup_variant_v4.1.0">r1041_e82_400bps_sup_variant_v4.1.0</option>
117 <option value="r1041_e82_400bps_sup_variant_v4.2.0">r1041_e82_400bps_sup_variant_v4.2.0</option>
118 <option value="r1041_e82_400bps_sup_variant_v4.3.0">r1041_e82_400bps_sup_variant_v4.3.0</option>
119 <option value="r1041_e82_400bps_sup_variant_v5.0.0">r1041_e82_400bps_sup_variant_v5.0.0</option>
78 <option value="r104_e81_fast_g5015">r104_e81_fast_g5015</option> 120 <option value="r104_e81_fast_g5015">r104_e81_fast_g5015</option>
121 <option value="r104_e81_fast_variant_g5015">r104_e81_fast_variant_g5015</option>
79 <option value="r104_e81_hac_g5015">r104_e81_hac_g5015</option> 122 <option value="r104_e81_hac_g5015">r104_e81_hac_g5015</option>
123 <option value="r104_e81_hac_variant_g5015">r104_e81_hac_variant_g5015</option>
80 <option value="r104_e81_sup_g5015">r104_e81_sup_g5015</option> 124 <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> 125 <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> 126 <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> 127 <option value="r941_e81_fast_g514">r941_e81_fast_g514</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> 128 <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> 129 <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> 130 <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> 131 <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> 132 <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> 133 <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> 134 <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> 135 <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> 136 <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> 137 <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> 138 <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> 139 <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> 140 <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> 141 <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> 142 <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> 143 <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> 144 <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> 145 <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> 146 <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> 147 <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> 148 <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> 149 <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> 150 <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> 151 <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> 152 <option value="r941_sup_plant_variant_g610">r941_sup_plant_variant_g610</option>
131 </param> 153 </param>
132 </xml> 154 </xml>
133 <xml name="reference"> 155 <xml name="reference">
175 197
176 :: 198 ::
177 199
178 {pore}_{device}_{caller variant}_{caller version} 200 {pore}_{device}_{caller variant}_{caller version}
179 201
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 202 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. 203 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.
182 204
183 ]]></token> 205 ]]></token>
184 206
185 <token name="@REFERENCES@"><![CDATA[ 207 <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>`_. 208 More information are available in the `github <https://github.com/nanoporetech/medaka>`_.
187 ]]></token> 209 ]]></token>
188 </macros> 210 </macros>