Mercurial > repos > xuebing > sharplabtool

comparison tools/ilmn_pacbio/smrtpipe_hybrid.xml @ 0:9071e359b9a3

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1 <tool id="smrtpipe_hybrid" name="AHA" version="1.0.0">
2 <description>Assemble contigs from a set of contigs and PacBio reads.</description>
3 <command interpreter="python">
4 smrtpipe_galaxy.py --nproc=24 --dat_extension=fasta --output=data/scaffold.fasta --galaxy_output=${outfile} ${iniFile}
5 </command>
6 <!--
7 <command>cp ${iniFile} ${outfile}</command>
8 -->
9 <inputs>
10 <param name="contigs" format="fasta" type="data" label="Starting Contigs"/>
11 <param name="reads" format="fasta" type="data" label="PacBio Reads"/>
12 <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/>
13 </inputs>
14 <configfiles>
15 <configfile name="iniFile">
16 [input]
17 assembled_contigs:${contigs}
18 file:${reads}
19
20 [HybridAssembly]
21 instrumentModel=RS
22 cleanup=False
23 untangler=pacbio
24 #set $schedule2 = $schedule.replace('X',';')
25 paramSchedule=${schedule2}
26 dontFillin=False
27 longReadsAsStrobe=True
28 exactQueryIds=True
29 rm4Opts=-minMatch 7 -minFrac 0.1 -minPctIdentity 65 -bestn 10 -noSplitSubreads
30 numberProcesses=16
31 cluster=False
32 minRepeatLength=100000
33 </configfile>
34 </configfiles>
35 <outputs>
36 <data name="outfile" format="fasta" label="Hybrid assembly contigs from ${on_string}"/>
37 </outputs>
38 <help>
39
40 **What it does**
41
42 The AHA assembly algorithm is an AMOS_-based pipeline
43 for finishing bacterial-sized
44 genomes using draft contigs and PacBio reads.
45
46 .. _AMOS: http://sourceforge.net/apps/mediawiki/amos
47
48 **Parameter list**
49
50 Parameter schedule
51 The parameter schedule is a semi-colon delimited list of triples. Each triple represents an iteration of hybrid assembly (alignment/scaffolding/gap-filling). The three paremeters for each iteration are the Z-score, number of reads required to define a link, and the minimum length of subreads used in links.
52
53 **Output**
54
55 FASTA file containing scaffolded and gap-filled contigs resulting from the
56 hybrid assembly.
57
58 </help>
59 </tool>