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comparison data_manager/kaiju_data_manager.xml @ 0:d89783920192 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/data_managers/data_manager_kaiju commit 59064c06143fdc7d7b17178e46911ba1009cd32e
author iuc
date Tue, 22 Apr 2025 14:02:32 +0000
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-1:000000000000 0:d89783920192
1 <tool id="kaiju_data_manager" name="kaiju data manager" tool_type="manage_data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
2 <description>builder</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.10.1</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">kaiju</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 #if $type.date == "today"
12 kaiju-makedb -s $type.select -t \${GALAXY_SLOTS:-1} &&
13 #else
14 #set year=str($type.date).split("-")[0]
15 wget https://kaiju-idx.s3.eu-central-1.amazonaws.com/${year}/kaiju_db_${type.select}_${type.date}.tgz --output-document=download.tgz &&
16 tar -xvf download.tgz &&
17 rm download.tgz &&
18 #end if
19 mkdir '${out_file.extra_files_path}' &&
20 mv \$(find . -name "*nodes.dmp") '${out_file.extra_files_path}'/nodes.dmp &&
21 mv \$(find . -name "*names.dmp") '${out_file.extra_files_path}'/names.dmp &&
22 mv \$(find . -name "*.fmi") '${out_file.extra_files_path}'/database.fmi &&
23 cp '$dmjson' '$out_file'
24 ]]></command>
25 <configfiles>
26 <configfile name="dmjson"><![CDATA[#slurp
27 #import datetime
28 #if $type.date == "today"
29 #set date = datetime.datetime.utcnow().strftime("%Y-%m-%d")
30 #else
31 #set date = $type.date
32 #end if
33 #if $type.select == "refseq"
34 #set name = "(refseq) bacterial, archaeal and viral genomes in the NCBI RefSeq database with assembly status Complete"
35 #elif $type.select == "refseq_nr"
36 #set name = "(refseq_nr) proteins from bacteria, Archaea, viruses, fungi and microbial eukaryotes from the NCBI RefSeq non-redundant proteins collection"
37 #elif $type.select == "refseq_ref"
38 #set name = "(refseq_ref) proteins from bacteria, Archaea from the NCBI RefSeq representative assemblies + viral proteins from NCBI RefSeq"
39 #elif $type.select == "progenomes"
40 #set name = "(progenomes) proteins in the set of representative genomes from the proGenomes v3 database and viral proteins from NCBI RefSeq"
41 #elif $type.select == "nr"
42 #set name = "(nr) NCBI BLAST non-redundant protein database 'nr', only Archaea, bacteria, and viruses"
43 #elif $type.select == "nr_euk"
44 #set name = "(nr_euk) nr and additionally including fungi and microbial eukaryotes"
45 #elif $type.select == "fungi"
46 #set name = "(fungi) all fungi genomes from NCBI RefSeq (any assembly status)"
47 #elif $type.select == "viruses"
48 #set name = "(viruses) viral genomes from NCBI RefSeq"
49 #elif $type.select == "plasmids"
50 #set name = "(plasmids) plasmid genomes from NCBI RefSeq"
51 #elif $type.select == "rvdb"
52 #set name = "(tvdb) viral proteins from RVDB-prot"
53 #end if
54 {
55 "data_tables":{
56 "kaiju":[
57 {
58 "value": "${date}_${$type.select}",
59 "name": "${date} $name",
60 "path": "output/",
61 "version": "@TOOL_VERSION@"
62 }
63 ]
64 }
65 }
66 ]]></configfile>
67 </configfiles>
68 <inputs>
69 <conditional name="type">
70 <param name="select" type="select" label="Source database" help="">
71 <option value="refseq">bacterial, archaeal and viral genomes in the NCBI RefSeq database with assembly status Complete</option>
72 <option value="refseq_nr">proteins from bacteria, Archaea, viruses, fungi and microbial eukaryotes from the NCBI RefSeq non-redundant proteins collection</option>
73 <option value="refseq_ref">proteins from bacteria, Archaea from the NCBI RefSeq representative assemblies + viral proteins from NCBI RefSeq</option>
74 <option value="progenomes">proteins in the set of representative genomes from the proGenomes v3 database and viral proteins from NCBI RefSeq</option>
75 <option value="nr">NCBI BLAST non-redundant protein database "nr", only Archaea, bacteria, and viruses</option>
76 <option value="nr_euk">nr and additionally including fungi and microbial eukaryotes</option>
77 <option value="fungi">All fungi genomes from NCBI RefSeq (any assembly status)</option>
78 <option value="viruses">Viral genomes from NCBI RefSeq</option>
79 <option value="plasmids">Plasmid genomes from NCBI RefSeq</option>
80 <option value="rvdb">Viral proteins from RVDB-prot</option>
81 </param>
82 <when value="refseq">
83 <param name="date" type="select" label="Date">
84 <option value="2024-08-14">2024-08-14</option>
85 <option value="today">Today</option>
86 </param>
87 </when>
88 <when value="refseq_nr">
89 <param name="date" type="select" label="Date">
90 <option value="2024-08-13">2024-08-13</option>
91 <option value="today">Today</option>
92 </param>
93 </when>
94 <when value="refseq_ref">
95 <param name="date" type="select" label="Date">
96 <option value="2024-08-14">2024-08-14</option>
97 <option value="today">Today</option>
98 </param>
99 </when>
100 <when value="progenomes">
101 <param name="date" type="select" label="Date">
102 <option value="2023-05-25">2023-05-25</option>
103 <option value="today">Today</option>
104 </param>
105 </when>
106 <when value="nr">
107 <param name="date" type="select" label="Date">
108 <option value="2024-08-25">2024-08-25</option>
109 <option value="today">Today</option>
110 </param>
111 </when>
112 <when value="nr_euk">
113 <param name="date" type="select" label="Date">
114 <option value="2023-05-10">2023-05-10</option>
115 <option value="today">Today</option>
116 </param>
117 </when>
118 <when value="fungi">
119 <param name="date" type="select" label="Date">
120 <option value="2024-08-16">2024-08-16</option>
121 <option value="today">Today</option>
122 </param>
123 </when>
124 <when value="viruses">
125 <param name="date" type="select" label="Date">
126 <option value="2024-08-15">2024-08-15</option>
127 <option value="today">Today</option>
128 </param>
129 </when>
130 <when value="plasmids">
131 <param name="date" type="select" label="Date">
132 <option value="2024-08-15">2024-08-15</option>
133 <option value="today">Today</option>
134 </param>
135 </when>
136 <when value="rvdb">
137 <param name="date" type="select" label="Date">
138 <option value="2024-12-20">2024-12-20</option>
139 <option value="today">Today</option>
140 </param>
141 </when>
142 </conditional>
143 </inputs>
144 <outputs>
145 <data name="out_file" format="data_manager_json"/>
146 </outputs>
147 <tests>
148 <test>
149 <conditional name="type">
150 <param name="select" value="viruses"/>
151 <param name="date" value="2024-08-15"/>
152 </conditional>
153 <output name="out_file">
154 <assert_contents>
155 <has_text text="kaiju"/>
156 <has_text text="(viruses)"/>
157 <has_text text="2024-08-15"/>
158 <has_text text="@TOOL_VERSION@"/>
159 </assert_contents>
160 </output>
161 </test>
162 <test>
163 <conditional name="type">
164 <param name="select" value="viruses"/>
165 <param name="date" value="today"/>
166 </conditional>
167 <output name="out_file">
168 <assert_contents>
169 <has_text text="kaiju"/>
170 <has_text text="(viruses)"/>
171 <has_text negate="true" text="2024-05-10"/>
172 <has_text text="@TOOL_VERSION@"/>
173 </assert_contents>
174 </output>
175 </test>
176 </tests>
177 <help><![CDATA[
178 .. class:: infomark
179
180 Download pre-built indices for kaiju. If a date is selected pre-built indices are downloaded from:
181 https://bioinformatics-centre.github.io/kaiju/downloads.html. Otherwise (i.e. if "today" is selected)
182 reference data is downloaded and an index is computed (which needs substantial ressources).
183 Pre-built indices might be preferrable in terms of reproducibility across Galaxy instances.
184
185 ]]></help>
186 <citations>
187 <citation type="doi">10.1038/ncomms11257</citation>
188 </citations>
189 </tool>