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comparison tools/mentalist_build.xml @ 0:071665c7c344 draft

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planemo upload
author dfornika
date Tue, 05 Sep 2017 18:52:15 -0400
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-1:000000000000 0:071665c7c344
1 <?xml version="1.0"?>
2 <tool id="mentalist_build" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.2">
3 <requirements>
4 <requirement type="package" version="0.1.2">mentalist</requirement>
5 </requirements>
6 <command detect_errors="exit_code">
7 <![CDATA[
8 mkdir mentalist-database && cd mentalist-database &&
9 MentaLiST.jl
10 build_db
11 --db '$kmer_database'
12 -k '$kmer_size'
13 #if $profile
14 -p '$profile'
15 #end if
16 -f ${" ".join(map(str, $input_fastas))} &&
17 cd .. &&
18 python '$__tool_directory__/make_json.py' --db '${database_name}' --out '${out_file}'
19 ]]>
20 </command>
21 <inputs>
22 <param name="kmer_size" type="integer"
23 label="Kmer size" help="Kmer size"
24 value="31" min="1" max="32" />
25 <param name="input_fastas" type="data_collection" collection_type="list" format="fasta" multiple="true"
26 label="Input Fasta" help="Fasta input files" />
27 <param name="profile" type="data" format="tsv" optional="true"
28 label="Profile" help="Profile for known genotypes" />
29 </inputs>
30 <outputs>
31 <data name="out_file" format="data_manager_json" />
32 </outputs>
33 <citations>
34 <citation type="doi">10.1101/172858</citation>
35 </citations>
36 </tool>