Mercurial > repos > mvdbeek > fermi2

comparison fermi2.xml @ 0:b808c0bc19a9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 47795b03c956d0f239aede8e27d2aa4e3c4c1d27
author mvdbeek
date Fri, 30 Dec 2016 10:25:59 -0500
parents
children adf010a51dde
comparison
equal deleted inserted replaced
-1:000000000000 0:b808c0bc19a9
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="r188">fermi2</requirement>
5 <requirement type="package" version="r181">bfc</requirement>
6 </requirements>
7 <command detect_errors="aggressive"><![CDATA[
8 fermi2.pl unitig
9 -s$genome_size
10 -t\${GALAXY_SLOTS:-4}
11 -l$readlength
12 -p prefix '$input1'
13 $T
14 $2
15 $E
16 > prefix.mak &&
17 make -f prefix.mak
18 ]]></command>
19 <inputs>
20 <param type="data" name="input1" format="fastqsanger,fastqsanger.gz"/>
21 <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/>
22 <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"/>
23 <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/>
24 <param argument="-2" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/>
25 <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/>
26 </inputs>
27 <outputs>
28 <data name="unitigs" format="fastqsanger.gz" from_work_dir="prefix.mag.gz"/>
29 </outputs>
30 <tests>
31 <test>
32 <param name="input1" value="test.fastq.gz"/>
33 <param name="readlength" value="150"/>
34 <param name="genome_size" value="1"/>
35 <output name="unitigs" file="unitigs.gz" compare="sim_size"/>
36 </test>
37 </tests>
38 <help><![CDATA[
39 fermi2 can assemble reads into unitigs.
40 Unitig output can be further analysed by alignment to a reference genome using bwa-mem,
41 and based on the alignment variants can be called using the fermi-variants tool.
42
43 ::
44
45 Usage: fermi2.pl unitig [options] <in.fq>
46
47 Options: -p STR output prefix [fmdef]
48 -s STR approximate genome size [100m]
49 -2 2-pass error correction
50 -l INT primary read length [101]
51 -T INT use INT-mer for post-trimming/filtering [61]
52 -k INT min overlap length during unitig construction [based on -l]
53 -o INT min overlap length during graph cleaning [based on -l]
54 -m INT min overlap length for unambiguous merging [based on -l]
55 -t INT number of threads [4]
56 -E don't apply error correction
57
58 ]]></help>
59 <citations>
60 <citation type="doi">10.1093/bioinformatics/btv440</citation>
61 </citations>
62 </tool>