Mercurial > repos > iuc > data_manager_mmseqs2_database

comparison data_manager/data_manager_mmseqs2_download.xml @ 2:35885ec2e59b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mmseqs2_database commit 611b90f1628037f05d85905c88629a422d0a2053
author iuc
date Mon, 14 Apr 2025 18:39:14 +0000
parents 75cc3fb4c10f
children
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equal deleted inserted replaced
1:561c4b181bfa 2:35885ec2e59b
1 <tool id="data_manager_mmseqs2_download" name="Download MMseqs2 databases" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05"> 1 <tool id="data_manager_mmseqs2_download" name="Download MMseqs2 databases" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" tool_type="manage_data" profile="22.05">
2 <description></description> 2 <description></description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">15.6f452</token> 4 <token name="@TOOL_VERSION@">17-b804f</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">mmseqs2</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">mmseqs2</requirement>
9 </requirements> 9 </requirements>
38 </configfile> 38 </configfile>
39 </configfiles> 39 </configfiles>
40 <inputs> 40 <inputs>
41 <conditional name="db_name"> 41 <conditional name="db_name">
42 <param argument="type" type="select" label="Type of Databases"> 42 <param argument="type" type="select" label="Type of Databases">
43 <option value="aminoacid">Aminoacid databases</option> 43 <option value="aminoacid">Aminoacid databases without taxonomy</option>
44 <option value="aminoacid_taxonomy">Aminoacid databases that can be used for taxonomy</option> 44 <option value="aminoacid_taxonomy">Aminoacid databases that can be used for taxonomy</option>
45 <option value="nucleotide">Nucleotide databases</option> 45 <option value="nucleotide">Nucleotide databases without taxonomy</option>
46 <option value="nucleotide_taxonomy">Nucleotide databases that can be used for taxonomy</option> 46 <option value="nucleotide_taxonomy">Nucleotide databases that can be used for taxonomy</option>
47 <option value="profile">Profile databases</option> 47 <option value="profile">Profile databases</option>
48 </param> 48 </param>
49 <when value="aminoacid"> 49 <when value="aminoacid">
50 <param name="db_type" value="aminoacid" type="hidden"/> 50 <param name="db_type" value="aminoacid" type="hidden"/>
51 <param name="db_taxonomy" value="no" type="hidden"/> 51 <param name="db_taxonomy" value="no" type="hidden"/>
52 <param name="database" type="select" label="MMseqs2 aminoacid databases"> 52 <param name="database" type="select" label="MMseqs2 aminoacid databases">
53 <option value="UniRef100" selected="true">UniRef100</option>
54 <option value="UniRef90">UniRef90</option>
55 <option value="UniRef50">UniRef50</option>
56 <option value="UniProtKB">UniProtKB</option>
57 <option value="UniProtKB/TrEMBL">TrEMBL (UniProtKB)</option>
58 <option value="UniProtKB/Swiss-Prot">Swiss-Prot (UniProtKB)</option>
59 <option value="NR">NR (Non-redundant protein sequences from GenPept, Swissprot, PIR, PDF, PDB, and NCBI RefSeq)</option>
60 <option value="GTDB">GTDB (Genome Taxonomy Database)</option>
61 <option value="PDB">PDB (The Protein Data Bank)</option> 53 <option value="PDB">PDB (The Protein Data Bank)</option>
62 </param> 54 </param>
63 </when> 55 </when>
64 <when value="aminoacid_taxonomy"> 56 <when value="aminoacid_taxonomy">
65 <param name="db_type" value="aminoacid" type="hidden"/> 57 <param name="db_type" value="aminoacid" type="hidden"/>
77 </when> 69 </when>
78 <when value="nucleotide"> 70 <when value="nucleotide">
79 <param name="db_type" value="nucleotide" type="hidden"/> 71 <param name="db_type" value="nucleotide" type="hidden"/>
80 <param name="db_taxonomy" value="no" type="hidden"/> 72 <param name="db_taxonomy" value="no" type="hidden"/>
81 <param name="database" type="select" label="MMseqs2 nucleotide databases"> 73 <param name="database" type="select" label="MMseqs2 nucleotide databases">
82 <option value="SILVA">SILVA</option>
83 <option value="Kalamari">Kalamari</option>
84 <option value="NT">NT (Partially non-redundant nucleotide sequences from all traditional divisions of GenBank, EMBL, and DDBJ excluding GSS, STS, PAT, EST, HTG, and WGS)</option> 74 <option value="NT">NT (Partially non-redundant nucleotide sequences from all traditional divisions of GenBank, EMBL, and DDBJ excluding GSS, STS, PAT, EST, HTG, and WGS)</option>
85 <option value="Resfinder">Resfinder</option> 75 <option value="Resfinder">Resfinder</option>
86 </param> 76 </param>
87 </when> 77 </when>
88 <when value="nucleotide_taxonomy"> 78 <when value="nucleotide_taxonomy">
120 <param name="database" value="SILVA" /> 110 <param name="database" value="SILVA" />
121 </conditional> 111 </conditional>
122 <output name="out_file"> 112 <output name="out_file">
123 <assert_contents> 113 <assert_contents>
124 <has_text text='"mmseqs2_databases":'/> 114 <has_text text='"mmseqs2_databases":'/>
125 <has_text text='"version": "15.6f452"'/> 115 <has_text text='"version": "@TOOL_VERSION@"'/>
126 <has_text_matching expression='"value": "SILVA-15.6f452-[0-9]{8}"'/> 116 <has_text_matching expression='"value": "SILVA-@TOOL_VERSION@-[0-9]{8}"'/>
127 <has_text_matching expression='"name": "SILVA [0-9]{8}"'/> 117 <has_text_matching expression='"name": "SILVA [0-9]{8}"'/>
128 <has_text text='"type": "nucleotide"'/> 118 <has_text text='"type": "nucleotide"'/>
129 <has_text text='"taxonomy": "yes"'/> 119 <has_text text='"taxonomy": "yes"'/>
130 <has_text text='"path": "SILVA"'/> 120 <has_text text='"path": "SILVA"'/>
131 </assert_contents> 121 </assert_contents>
139 <param name="database" value="UniProtKB/Swiss-Prot" /> 129 <param name="database" value="UniProtKB/Swiss-Prot" />
140 </conditional> 130 </conditional>
141 <output name="out_file"> 131 <output name="out_file">
142 <assert_contents> 132 <assert_contents>
143 <has_text text='"mmseqs2_databases":'/> 133 <has_text text='"mmseqs2_databases":'/>
144 <has_text text='"version": "15.6f452"'/> 134 <has_text text='"version": "@TOOL_VERSION@"'/>
145 <has_text_matching expression='"value": "UniProtKB/Swiss-Prot-15.6f452-[0-9]{8}"'/> 135 <has_text_matching expression='"value": "UniProtKB/Swiss-Prot-@TOOL_VERSION@-[0-9]{8}"'/>
146 <has_text_matching expression='"name": "UniProtKB/Swiss-Prot [0-9]{8}"'/> 136 <has_text_matching expression='"name": "UniProtKB/Swiss-Prot [0-9]{8}"'/>
147 <has_text text='"type": "aminoacid"'/> 137 <has_text text='"type": "aminoacid"'/>
148 <has_text text='"taxonomy": "yes"'/> 138 <has_text text='"taxonomy": "yes"'/>
149 <has_text text='"path": "Swiss-Prot"'/> 139 <has_text text='"path": "Swiss-Prot"'/>
150 </assert_contents> 140 </assert_contents>