annotate edena_ass_wrapper.xml @ 0:60609a9cef3b draft

Uploaded
author crs4
date Mon, 09 Sep 2013 05:44:31 -0400
parents
children cd6cc6d76708
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
60609a9cef3b Uploaded
crs4
parents:
diff changeset
1 <tool id="edena_ass_wrapper" name="Edena (assembling)" version="0.2.1">
60609a9cef3b Uploaded
crs4
parents:
diff changeset
2 <description></description>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
3 <requirements>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
4 <requirement type="package" version="3.130110">edena</requirement>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
5 </requirements>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
6 <version_command>edena -v</version_command>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
7 <command interpreter="python">
60609a9cef3b Uploaded
crs4
parents:
diff changeset
8 edena_ass_wrapper.py --ovl_input=$ovl_input
60609a9cef3b Uploaded
crs4
parents:
diff changeset
9 #if str($overlapCutoff)
60609a9cef3b Uploaded
crs4
parents:
diff changeset
10 --overlapCutoff=$overlapCutoff
60609a9cef3b Uploaded
crs4
parents:
diff changeset
11 #end if
60609a9cef3b Uploaded
crs4
parents:
diff changeset
12 #if $cc
60609a9cef3b Uploaded
crs4
parents:
diff changeset
13 --cc
60609a9cef3b Uploaded
crs4
parents:
diff changeset
14 #end if
60609a9cef3b Uploaded
crs4
parents:
diff changeset
15 #if $discardNonUsable
60609a9cef3b Uploaded
crs4
parents:
diff changeset
16 --discardNonUsable
60609a9cef3b Uploaded
crs4
parents:
diff changeset
17 #end if
60609a9cef3b Uploaded
crs4
parents:
diff changeset
18 #if str($minContigSize)
60609a9cef3b Uploaded
crs4
parents:
diff changeset
19 --minContigSize=$minContigSize
60609a9cef3b Uploaded
crs4
parents:
diff changeset
20 #end if
60609a9cef3b Uploaded
crs4
parents:
diff changeset
21 #if str($minCoverage)
60609a9cef3b Uploaded
crs4
parents:
diff changeset
22 --minCoverage=$minCoverage
60609a9cef3b Uploaded
crs4
parents:
diff changeset
23 #end if
60609a9cef3b Uploaded
crs4
parents:
diff changeset
24 #if str($trim)
60609a9cef3b Uploaded
crs4
parents:
diff changeset
25 --trim=$trim
60609a9cef3b Uploaded
crs4
parents:
diff changeset
26 #end if
60609a9cef3b Uploaded
crs4
parents:
diff changeset
27 #if str($peHorizon)
60609a9cef3b Uploaded
crs4
parents:
diff changeset
28 --peHorizon=$peHorizon
60609a9cef3b Uploaded
crs4
parents:
diff changeset
29 #end if
60609a9cef3b Uploaded
crs4
parents:
diff changeset
30 --covStats=$covStats --out_contigs_cov=$out_contigs_cov --out_contigs_fasta=$out_contigs_fasta --out_contigs_lay=$out_contigs_lay --out_log_txt=$out_log_txt --out_nodesInfo=$out_nodesInfo --out_nodesPosition=$out_nodesPosition
60609a9cef3b Uploaded
crs4
parents:
diff changeset
31 --logfile=$logfile
60609a9cef3b Uploaded
crs4
parents:
diff changeset
32 </command>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
33
60609a9cef3b Uploaded
crs4
parents:
diff changeset
34 <inputs>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
35 <param name="ovl_input" type="data" format="ovl" label="Edena .ovl file (-e)" help="Specify here the Edena “.ovl” file obtained from the overlapping step" />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
36
60609a9cef3b Uploaded
crs4
parents:
diff changeset
37 <param name="overlapCutoff" type="integer" value="" optional="true" label="Overlap cutoff (-m)" help="The overlap cutoff is by default set to half of the reads length L (see the log output by the overlapping step to identify it). It is however still worth trying to increase this setting since it can greatly simplify highly connected overlaps graphs, and thus speed up the assembly. If one step during the assembly hangs, increasing the overlap cutoff is the first thing to do." />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
38
60609a9cef3b Uploaded
crs4
parents:
diff changeset
39 <param name="cc" type="boolean" checked="true" label="Contextual cleaning (-cc)" help="This option is enabled by default. Contextual cleaning is a procedure that efficiently identifies and removes false positive edges, improving thus the assembly. This procedure can be seen as a dynamic overlap cutoff on the overlaps graph. It is possible however for this step to be slow on ultra-high covered sequencing data. In such cases, try to increase the overlap cutoff value, or to simply disable this option." />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
40
60609a9cef3b Uploaded
crs4
parents:
diff changeset
41 <param name="discardNonUsable" type="boolean" checked="true" label="Discard non usable nodes (-discardNonUsable)" help="Enabled by default, this procedure discards nodes smaller than 1.5*readLength and that are not connected to any other nodes." />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
42
60609a9cef3b Uploaded
crs4
parents:
diff changeset
43 <param name="minContigSize" type="integer" value="" optional="true" label="Minimum size of the contigs to output (-c)" help="If not specified, this value is set to 1.5*readLength." />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
44
60609a9cef3b Uploaded
crs4
parents:
diff changeset
45 <param name="minCoverage" type="float" value="" optional="true" label="Minimum required coverage for the contigs (-minCoverage)" help="If not specified, this value is automatically determined from the nodes coverage distribution. This estimation however supposes a uniform coverage. It could be worth overriding this parameter in some cases, i.e. with transcriptome data, or a mix of PCR product assemblies." />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
46
60609a9cef3b Uploaded
crs4
parents:
diff changeset
47 <param name="trim" type="integer" value="4" optional="true" label="Coverage cutoff for contigs ends (-trim)" help="Contig interruptions are caused either because of a non-resolved ambiguity, or because of a lack of overlapping reads. In the latter case, the contig end may be inaccurate. This option will trim such ends until a minimum coverage is reached. By default, this value is set to 4. To disable contigs ends trimming, set this value to 1." />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
48
60609a9cef3b Uploaded
crs4
parents:
diff changeset
49 <param name="peHorizon" type="integer" value="" optional="true" label="Maximum search distance for paired-end reads connection (-peHorizon)" help="Edena samples the overlaps graph to accurately determine the paired distance distribution. This parameter specifies the maximum distance that is searched during this sampling. By default, this value is set to 1000 if solely direct-reverse mates are used and 10000 if reverse-direct mates are also used. This value has to be set to at least 2X the expected size of the longest mate library." />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
50 </inputs>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
51
60609a9cef3b Uploaded
crs4
parents:
diff changeset
52 <outputs>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
53 <data name="covStats" format="tabular" label="${tool.name} on ${on_string}: CovStats" />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
54 <data name="out_contigs_cov" format="txt" label="${tool.name} on ${on_string}: ContigsCov" />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
55 <data name="out_contigs_fasta" format="fasta" label="${tool.name} on ${on_string}: ContigsFasta" />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
56 <data name="out_contigs_lay" format="txt" label="${tool.name} on ${on_string}: ContigsLay" />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
57 <data name="out_log_txt" format="txt" label="${tool.name} on ${on_string}: log" />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
58 <data name="out_nodesInfo" format="txt" label="${tool.name} on ${on_string}: nodes info" />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
59 <data name="out_nodesPosition" format="txt" label="${tool.name} on ${on_string}: nodes position" />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
60 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log (terminal)" />
60609a9cef3b Uploaded
crs4
parents:
diff changeset
61 </outputs>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
62
60609a9cef3b Uploaded
crs4
parents:
diff changeset
63 <tests>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
64
60609a9cef3b Uploaded
crs4
parents:
diff changeset
65 </tests>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
66 <help>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
67 **What it does**
60609a9cef3b Uploaded
crs4
parents:
diff changeset
68
60609a9cef3b Uploaded
crs4
parents:
diff changeset
69 The key parameter for this mode is the overlaps size cutoff (option –m). By default it is set to half of the reads length, which is quite conservative. If your sequencing project is well covered (>50-100x) you may try increasing a bit this value. The minCoverage is an important parameter which is automatically determined. You may check this value in the program output and possibly override it.
60609a9cef3b Uploaded
crs4
parents:
diff changeset
70
60609a9cef3b Uploaded
crs4
parents:
diff changeset
71 **License and citation**
60609a9cef3b Uploaded
crs4
parents:
diff changeset
72
60609a9cef3b Uploaded
crs4
parents:
diff changeset
73 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
60609a9cef3b Uploaded
crs4
parents:
diff changeset
74
60609a9cef3b Uploaded
crs4
parents:
diff changeset
75 .. _CRS4 Srl.: http://www.crs4.it/
60609a9cef3b Uploaded
crs4
parents:
diff changeset
76 .. _MIT license: http://opensource.org/licenses/MIT
60609a9cef3b Uploaded
crs4
parents:
diff changeset
77
60609a9cef3b Uploaded
crs4
parents:
diff changeset
78 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
60609a9cef3b Uploaded
crs4
parents:
diff changeset
79
60609a9cef3b Uploaded
crs4
parents:
diff changeset
80 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted*
60609a9cef3b Uploaded
crs4
parents:
diff changeset
81 .. _Cuccuru2013: http://orione.crs4.it/
60609a9cef3b Uploaded
crs4
parents:
diff changeset
82
60609a9cef3b Uploaded
crs4
parents:
diff changeset
83 This tool uses `Edena`_, which is licensed separately. Please cite |Hernandez2008|_.
60609a9cef3b Uploaded
crs4
parents:
diff changeset
84
60609a9cef3b Uploaded
crs4
parents:
diff changeset
85 .. _Edena: http://www.genomic.ch/edena.php
60609a9cef3b Uploaded
crs4
parents:
diff changeset
86 .. |Hernandez2008| replace:: Hernandez, D., *et al.* (2008) De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer. *Genome Res.* 18(5), 802-809
60609a9cef3b Uploaded
crs4
parents:
diff changeset
87 .. _Hernandez2008: http://genome.cshlp.org/content/18/5/802
60609a9cef3b Uploaded
crs4
parents:
diff changeset
88 </help>
60609a9cef3b Uploaded
crs4
parents:
diff changeset
89 </tool>