Mercurial > repos > iuc > fermi2
annotate fermi2.xml @ 0:b59546214e63 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
author | iuc |
---|---|
date | Thu, 05 Jan 2017 08:35:31 -0500 |
parents | |
children | 06d22a2d3c64 |
rev | line source |
---|---|
0
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
1 <tool id="fermi2" name="fermi2" version="0.14.dev1"> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
2 <description>assembles Illumina reads into unitigs</description> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
3 <requirements> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
4 <requirement type="package" version="r193">fermi2</requirement> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
5 </requirements> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
6 <command detect_errors="aggressive"><![CDATA[ |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
7 fermi2.pl unitig |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
8 -s$genome_size |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
9 -t\${GALAXY_SLOTS:-4} |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
10 -l$readlength |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
11 -p prefix "cat |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
12 #for fastq in $input1: |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
13 '$fastq' |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
14 #end for |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
15 " |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
16 -T $T |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
17 $two_pass_error |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
18 $E |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
19 > prefix.mak && |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
20 make -f prefix.mak |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
21 ]]></command> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
22 <inputs> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
23 <param type="data" multiple="true" name="input1" format="fastqsanger,fastqsanger.gz"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
24 <param argument="-l" name="readlength" type="integer" label="primary read length" value="101" min="70"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
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"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
26 <param argument="-T" type="integer" value="61" label="use INT-mer for post-trimming/filtering" min="10"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
27 <param argument="-2" name="two_pass_error" type="boolean" checked="false" truevalue="-2" falsevalue="" label="Use 2-pass error correction"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
28 <param argument="-E" type="boolean" checked="false" truevalue="-E" falsevalue="" label="Do not apply error correction"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
29 </inputs> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
30 <outputs> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
31 <data name="unitigs" format="fastqsanger.gz" from_work_dir="prefix.mag.gz"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
32 </outputs> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
33 <tests> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
34 <test> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
35 <param name="input1" value="test.fastq.gz,test.fastq.gz"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
36 <param name="readlength" value="150"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
37 <param name="genome_size" value="1"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
38 <output name="unitigs" file="unitigs.gz" compare="sim_size"/> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
39 </test> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
40 </tests> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
41 <help><![CDATA[ |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
42 fermi2 can assemble reads into unitigs. |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
43 Unitig output can be further analysed by alignment to a reference genome using bwa-mem, |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
44 and based on the alignment variants can be called using the fermi-variants tool. |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
45 |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
46 :: |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
47 |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
48 Usage: fermi2.pl unitig [options] <in.fq> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
49 |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
50 Options: -p STR output prefix [fmdef] |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
51 -s STR approximate genome size [100m] |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
52 -2 2-pass error correction |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
53 -l INT primary read length [101] |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
54 -T INT use INT-mer for post-trimming/filtering [61] |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
55 -k INT min overlap length during unitig construction [based on -l] |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
56 -o INT min overlap length during graph cleaning [based on -l] |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
57 -m INT min overlap length for unambiguous merging [based on -l] |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
58 -t INT number of threads [4] |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
59 -E don't apply error correction |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
60 |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
61 ]]></help> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
62 <citations> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
63 <citation type="doi">10.1093/bioinformatics/btv440</citation> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
64 </citations> |
b59546214e63
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit 16dcfc0fb84fad80fcf18417ae46c5499c96147a
iuc
parents:
diff
changeset
|
65 </tool> |