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comparison fermi2.xml @ 0:556001c80d75 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
author iuc
date Thu, 05 Jan 2017 08:35:03 -0500
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1 <tool id="fermi2" name="fermi2" version="0.14.dev1">
2 <description>assembles Illumina reads into unitigs</description>
3 <requirements>
4 <requirement type="package" version="r193">fermi2</requirement>
5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[
7 fermi2.pl unitig
8 -s$genome_size
9 -t\${GALAXY_SLOTS:-4}
10 -l$readlength
11 -p prefix "cat
12 #for fastq in $input1:
13 '$fastq'
14 #end for
15 "
16 -T $T
17 $two_pass_error
18 $E
19 > prefix.mak &&
20 make -f prefix.mak
21 ]]></command>
22 <inputs>
23 <param type="data" multiple="true" name="input1" format="fastqsanger,fastqsanger.gz"/>
24 <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/>
25 <param argument="-s" name="genome_size" type="integer" value="180000" min="1" label="approximate genome size in kilobases" help="Enter approximate genome size in kilobases. For a human genome of 3.2 gigabases enter 3200000"/>
26 <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/>
27 <param argument="-2" name="two_pass_error" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/>
28 <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/>
29 </inputs>
30 <outputs>
31 <data name="unitigs" format="fastqsanger.gz" from_work_dir="prefix.mag.gz"/>
32 </outputs>
33 <tests>
34 <test>
35 <param name="input1" value="test.fastq.gz,test.fastq.gz"/>
36 <param name="readlength" value="150"/>
37 <param name="genome_size" value="1"/>
38 <output name="unitigs" file="unitigs.gz" compare="sim_size"/>
39 </test>
40 </tests>
41 <help><![CDATA[
42 fermi2 can assemble reads into unitigs.
43 Unitig output can be further analysed by alignment to a reference genome using bwa-mem,
44 and based on the alignment variants can be called using the fermi-variants tool.
45
46 ::
47
48 Usage: fermi2.pl unitig [options] <in.fq>
49
50 Options: -p STR output prefix [fmdef]
51 -s STR approximate genome size [100m]
52 -2 2-pass error correction
53 -l INT primary read length [101]
54 -T INT use INT-mer for post-trimming/filtering [61]
55 -k INT min overlap length during unitig construction [based on -l]
56 -o INT min overlap length during graph cleaning [based on -l]
57 -m INT min overlap length for unambiguous merging [based on -l]
58 -t INT number of threads [4]
59 -E don't apply error correction
60
61 ]]></help>
62 <citations>
63 <citation type="doi">10.1093/bioinformatics/btv440</citation>
64 </citations>
65 </tool>