PageRenderTime 36ms CodeModel.GetById 32ms app.highlight 1ms RepoModel.GetById 1ms app.codeStats 0ms

/tools/ilmn_pacbio/smrtpipe_hybrid.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 59 lines | 47 code | 9 blank | 3 comment | 0 complexity | 586189e7fad02b485dba12cb6e51a687 MD5 | raw file
 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} ${outfile}</command>
 8  -->
 9  <inputs>
10    <param name="contigs" format="fasta" type="data" label="Starting Contigs"/>
11    <param name="reads" format="fasta" type="data" label="PacBio Reads"/>
12    <param name="schedule" type="text" value="6,3,75;6,3,75;5,3,75;5,3,75;6,2,75;6,2,75;5,2,75;5,2,75" label="Parameter Schedule" size="60"/>
13  </inputs>
14  <configfiles>
15    <configfile name="iniFile">
16[input]
17assembled_contigs:${contigs}
18file:${reads}
19
20[HybridAssembly]
21instrumentModel=RS
22cleanup=False
23untangler=pacbio
24#set $schedule2 = $schedule.replace('X',';')
25paramSchedule=${schedule2}
26dontFillin=False
27longReadsAsStrobe=True
28exactQueryIds=True
29rm4Opts=-minMatch 7 -minFrac 0.1 -minPctIdentity 65 -bestn 10 -noSplitSubreads
30numberProcesses=16
31cluster=False
32minRepeatLength=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
42The AHA assembly algorithm is an AMOS_-based pipeline
43for finishing bacterial-sized
44genomes using draft contigs and PacBio reads.
45
46.. _AMOS: http://sourceforge.net/apps/mediawiki/amos
47
48**Parameter list**
49
50Parameter 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
55FASTA file containing scaffolded and gap-filled contigs resulting from the 
56hybrid assembly.
57
58  </help>
59</tool>