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comparison minia.xml @ 0:8a6ff5a83a29 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/minia commit cd3b054df45f2805457941fa09170389f99df80e"
author iuc
date Thu, 09 Apr 2020 06:34:49 +0000
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children 553cf3df936c
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-1:000000000000 0:8a6ff5a83a29
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>