Mercurial > repos > iuc > minia
comparison minia.xml @ 0:0a66ef6dacb7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
author | iuc |
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date | Thu, 09 Apr 2020 03:42:24 -0400 |
parents | |
children | b2dc51639ad5 |
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-1:000000000000 | 0:0a66ef6dacb7 |
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1 <tool id="minia" name="Minia" version="@TOOL_VERSION@"> | |
2 <description>Short-read assembler based on a de Bruijn graph</description> | |
3 <macros> | |
4 <token name="@TOOL_VERSION@">3.2.1</token> | |
5 </macros> | |
6 <requirements> | |
7 <requirement type="package" version="@TOOL_VERSION@">minia</requirement> | |
8 </requirements> | |
9 <command detect_errors="exit_code"><![CDATA[ | |
10 #set input = 'infile.' + $in.ext | |
11 ln -s '$in' '$input' && | |
12 | |
13 minia | |
14 -in '$input' | |
15 -kmer-size $kmer_size | |
16 #if str($abundance_min): | |
17 -abundance-min $abundance_min | |
18 #end if | |
19 #if str($abundance_max): | |
20 -abundance-min $abundance_max | |
21 #end if | |
22 -nb-cores \${GALAXY_SLOTS:-1} | |
23 -out output | |
24 ]]></command> | |
25 <inputs> | |
26 <param argument="-in" type="data" format="fasta,fastqsanger,fastqsanger.gz,fasta.gz" label="Reads in FASTA or FASTQ format" /> | |
27 <param argument="-kmer-size" type="integer" value="31" min="1" label="Size of a kmer" /> | |
28 <param argument="-abundance-min" type="integer" value="" optional="true" min="0" label="Min abundance threshold for solid kmers (default: 2)" /> | |
29 <param argument="-abundance-max" type="integer" value="" optional="true" label="Max abundance threshold for solid kmers" /> | |
30 </inputs> | |
31 <outputs> | |
32 <data name="output" format="fasta" label="${tool.name} on ${on_string}" from_work_dir="output.contigs.fa" /> | |
33 </outputs> | |
34 <tests> | |
35 <test> | |
36 <param name="in" value="ec.fa" /> | |
37 <param name="kmer_size" value="21" /> | |
38 <param name="abundance_min" value="1" /> | |
39 <output name="output" ftype="fasta"> | |
40 <assert_contents> | |
41 <has_text text="LN:i:460 KC:i:2200 km:f:5.000"/> | |
42 <has_text text="LN:i:637 KC:i:3085 km:f:5.000"/> | |
43 <has_n_lines n="4"/> | |
44 </assert_contents> | |
45 </output> | |
46 </test> | |
47 </tests> | |
48 <help><![CDATA[ | |
49 Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. | |
50 The output of Minia is a set of contigs. | |
51 ]]></help> | |
52 <citations> | |
53 <citation type="doi">10.1186/1748-7188-8-22</citation> | |
54 </citations> | |
55 </tool> |