Mercurial > repos > iuc > data_manager_build_bracken_database

comparison data_manager/bracken_build_database.xml @ 3:3c7d2c84cb09 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
author iuc
date Mon, 08 Nov 2021 15:51:51 +0000
parents 9059edc96a85
children 5c8a23ccb14a
comparison
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2:fd5830f88314 3:3c7d2c84cb09
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5+galaxy0" profile="19.01"> 2 <tool id="bracken_build_database" name="Bracken Database Builder" tool_type="manage_data" version="2.5+galaxy1" profile="19.01">
3 <description>bracken database builder</description> 3 <description>bracken database builder</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.5">bracken</requirement> 5 <requirement type="package" version="2.5">bracken</requirement>
6 <requirement type="package" version="2.0.8_beta">kraken2</requirement> 6 <requirement type="package" version="2.1.1">kraken2</requirement>
7 </requirements> 7 </requirements>
8 <command> 8 <command>
9 <![CDATA[ 9 <![CDATA[
10 #import os 10 #import os
11 #set db_dir = os.path.basename($kraken_db.fields.path) 11 #set db_dir = os.path.basename($kraken_db.fields.path)
12 12
13 mkdir '$db_dir' && 13 mkdir '$db_dir' &&
14 ln -s '${kraken_db.fields.path}'/* '$db_dir/' && 14 ln -s '${kraken_db.fields.path}/*' '$db_dir/' &&
15 python '$__tool_directory__/bracken_build_database.py' 15 python '$__tool_directory__/bracken_build_database.py'
16 '${out_file}' 16 '${out_file}'
17 --kraken-db '$db_dir' 17
18 --threads \${GALAXY_SLOTS:-1} 18 --threads \${GALAXY_SLOTS:-1}
19 --kmer-len ${kmer_len} 19 #if $check_prebuilt.prebuilt == "no"
20 --read-len ${read_len} 20 --kraken-db '$db_dir'
21 --kmer-len ${check_prebuilt.kmer_len}
22 #end if
23 #if $check_prebuilt.prebuilt == "yes"
24 --kraken-db '${kraken_db.fields.path}'
25 --prebuilt
26 #end if
27 --read-len ${check_prebuilt.read_len}
21 --database-name '${database_name}' 28 --database-name '${database_name}'
22 ]]> 29 ]]>
23 </command> 30 </command>
24 <inputs> 31 <inputs>
25 <param name="kraken_db" type="select"> 32 <param name="kraken_db" type="select">
26 <options from_data_table="kraken2_databases"> 33 <options from_data_table="kraken2_databases">
27 <validator type="no_options" message="No Kraken2 databases are available" /> 34 <validator type="no_options" message="No Kraken2 databases are available" />
28 </options> 35 </options>
29 </param> 36 </param>
30 <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" /> 37 <conditional name="check_prebuilt">
31 <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" /> 38 <param name="prebuilt" type="select" label="Use Pre-built DB">
32 <param name="database_name" type="text" label="Database Name" /> 39 <option value="no">No</option>
40 <option value="yes">Yes</option>
41 </param>
42 <when value="no">
43 <param name="kmer_len" type="integer" min="8" max="256" value="35" label="K-mer length" />
44 <param name="read_len" type="integer" min="8" max="1000" value="100" label="Read length" />
45 </when>
46 <when value="yes">
47 <param name="read_len" type="select" label="Read length" >
48 <option value="50">50</option>
49 <option value="75">75</option>
50 <option value="100">100</option>
51 <option value="150">150</option>
52 <option value="200">200</option>
53 <option value="250">250</option>
54 <option value="300">300</option>
55 </param>
56 </when>
57 </conditional>
58 <param name="database_name" type="text" label="Database Name" />
33 </inputs> 59 </inputs>
34 <outputs> 60 <outputs>
35 <data name="out_file" format="data_manager_json" /> 61 <data name="out_file" format="data_manager_json" />
36 </outputs> 62 </outputs>
37 <tests> 63 <tests>