Mercurial > repos > iuc > fermi2
comparison fermi2.xml @ 0:b59546214e63 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
author | iuc |
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date | Thu, 05 Jan 2017 08:35:31 -0500 |
parents | |
children | 06d22a2d3c64 |
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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> |