edena: edena_ass_wrapper.xml annotate

annotate edena_ass_wrapper.xml @ 2:b8c6a38530eb draft default tip

Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA _SITE_OPTIONS. Directly call edena, remove edena_ovl_wrapper.py and edena_ass_wrapper.py . Discard stderr instead of redirecting to stdout. Do not redirect stdout to logfile. Add readme.rst .

author	crs4
date	Fri, 31 Jan 2014 12:08:21 -0500
parents	cd6cc6d76708
children

rev	line source
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	1 <tool id="edena_ass_wrapper" name="Edena (assembling)" version="0.3">
0 60609a9cef3b Uploaded crs4 parents: diff changeset	2 <description></description>
60609a9cef3b Uploaded crs4 parents: diff changeset	3 <requirements>
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	4 <requirement type="package" version="3.131028">edena</requirement>
0 60609a9cef3b Uploaded crs4 parents: diff changeset	5 </requirements>
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	6 <version_command>edena \| head -n 1</version_command>
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	7 <command>
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	8 edena -e $ovl_input
0 60609a9cef3b Uploaded crs4 parents: diff changeset	9 #if str($overlapCutoff)
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	10 -m $overlapCutoff
0 60609a9cef3b Uploaded crs4 parents: diff changeset	11 #end if
60609a9cef3b Uploaded crs4 parents: diff changeset	12 #if $cc
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	13 -cc yes
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	14 #else
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	15 -cc no
0 60609a9cef3b Uploaded crs4 parents: diff changeset	16 #end if
60609a9cef3b Uploaded crs4 parents: diff changeset	17 #if $discardNonUsable
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	18 -discardNonUsable yes
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	19 #else
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	20 -discardNonUsable no
0 60609a9cef3b Uploaded crs4 parents: diff changeset	21 #end if
60609a9cef3b Uploaded crs4 parents: diff changeset	22 #if str($minContigSize)
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	23 -c $minContigSize
0 60609a9cef3b Uploaded crs4 parents: diff changeset	24 #end if
60609a9cef3b Uploaded crs4 parents: diff changeset	25 #if str($minCoverage)
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	26 -minCoverage $minCoverage
0 60609a9cef3b Uploaded crs4 parents: diff changeset	27 #end if
60609a9cef3b Uploaded crs4 parents: diff changeset	28 #if str($trim)
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	29 -trim $trim
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	30 #end if
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	31 #if str($sph)
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	32 -sph $sph
0 60609a9cef3b Uploaded crs4 parents: diff changeset	33 #end if
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	34 #if str($lph)
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	35 -lph $lph
0 60609a9cef3b Uploaded crs4 parents: diff changeset	36 #end if
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	37 2>/dev/null ## need to discard stderr because edena writes some progress info there (e.g. "Condensing overlaps graph...")
0 60609a9cef3b Uploaded crs4 parents: diff changeset	38 </command>
60609a9cef3b Uploaded crs4 parents: diff changeset	39
60609a9cef3b Uploaded crs4 parents: diff changeset	40 <inputs>
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	41 <param name="ovl_input" type="data" format="ovl" label="Edena overlap (.ovl) file (-e)" help="Specify here the Edena “.ovl” file obtained from the overlapping step" />
0 60609a9cef3b Uploaded crs4 parents: diff changeset	42
60609a9cef3b Uploaded crs4 parents: diff changeset	43 <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	44
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	45 <param name="cc" type="boolean" checked="true" label="Contextual cleaning of spurious edges (-cc)" help="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." />
0 60609a9cef3b Uploaded crs4 parents: diff changeset	46
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	47 <param name="discardNonUsable" type="boolean" checked="true" label="Discard non usable nodes (-discardNonUsable)" help="This procedure discards orphan nodes smaller than 1.5*readLength." />
0 60609a9cef3b Uploaded crs4 parents: diff changeset	48
60609a9cef3b Uploaded crs4 parents: diff changeset	49 <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	50
60609a9cef3b Uploaded crs4 parents: diff changeset	51 <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	52
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	53 <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 a few bases from these 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." />
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	54 <param name="sph" type="integer" value="1000" optional="true" label="Maximum search distance for paired-end (forward-reverse) sampling (-sph)" 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. This value has to be set to at least 2X the expected size of the longest paired-end library." />
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	55 <param name="lph" type="integer" value="15000" optional="true" label="Maximum search distance for mate-pair (reverse-forward) sampling (-lph)" 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. This value has to be set to at least 2X the expected size of the longest mate-pair library." />
0 60609a9cef3b Uploaded crs4 parents: diff changeset	56 </inputs>
60609a9cef3b Uploaded crs4 parents: diff changeset	57
60609a9cef3b Uploaded crs4 parents: diff changeset	58 <outputs>
2 b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	59 <data name="out_contigs_cov" format="txt" label="${tool.name} on ${on_string}: ContigsCov" from_work_dir="out_contigs.cov" />
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	60 <data name="out_contigs_fasta" format="fasta" label="${tool.name} on ${on_string}: ContigsFasta" from_work_dir="out_contigs.fasta" />
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	61 <data name="out_contigs_lay" format="txt" label="${tool.name} on ${on_string}: ContigsLay" from_work_dir="out_contigs.lay" />
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	62 <data name="out_log_txt" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="out_assembling.log" />
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	63 <data name="out_nodesInfo" format="txt" label="${tool.name} on ${on_string}: nodes info" from_work_dir="out_nodesInfo" />
b8c6a38530eb Support Edena v. 3.131028 (new <version_command>, official overlapping log file, covStats output file removed, -lph and -sph options instead of -peHorizon). Use $GALAXY_SLOTS instead of $EDENA crs4 parents: 1 diff changeset	64 <data name="out_nodesPosition" format="txt" label="${tool.name} on ${on_string}: nodes position" from_work_dir="out_nodesPosition" />
0 60609a9cef3b Uploaded crs4 parents: diff changeset	65 </outputs>
60609a9cef3b Uploaded crs4 parents: diff changeset	66
60609a9cef3b Uploaded crs4 parents: diff changeset	67 <tests>
60609a9cef3b Uploaded crs4 parents: diff changeset	68
60609a9cef3b Uploaded crs4 parents: diff changeset	69 </tests>
60609a9cef3b Uploaded crs4 parents: diff changeset	70 <help>
60609a9cef3b Uploaded crs4 parents: diff changeset	71 What it does
60609a9cef3b Uploaded crs4 parents: diff changeset	72
1 cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	73 Edena is an overlaps graph based short reads assembler and is suited to Illumina GA reads. An assembly with Edena is a two step process: overlapping and assembling.
cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	74
cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	75 In the assembling step, the overlapping file (produced in the previous step) is provided to the program, as well as some assembly parameters. A set of contigs in FASTA format is outputted. The purpose of having a two step process is that the overlapping file is computed only once and can then be used to produce assemblies with different parameters.
cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	76
cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	77 The key parameter for this step 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.
0 60609a9cef3b Uploaded crs4 parents: diff changeset	78
60609a9cef3b Uploaded crs4 parents: diff changeset	79 License and citation
60609a9cef3b Uploaded crs4 parents: diff changeset	80
60609a9cef3b Uploaded crs4 parents: diff changeset	81 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
60609a9cef3b Uploaded crs4 parents: diff changeset	82
60609a9cef3b Uploaded crs4 parents: diff changeset	83 .. _CRS4 Srl.: http://www.crs4.it/
60609a9cef3b Uploaded crs4 parents: diff changeset	84 .. _MIT license: http://opensource.org/licenses/MIT
60609a9cef3b Uploaded crs4 parents: diff changeset	85
60609a9cef3b Uploaded crs4 parents: diff changeset	86 If you use this tool in Galaxy, please cite \|Cuccuru2013\|_.
60609a9cef3b Uploaded crs4 parents: diff changeset	87
60609a9cef3b Uploaded crs4 parents: diff changeset	88 .. \|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	89 .. _Cuccuru2013: http://orione.crs4.it/
60609a9cef3b Uploaded crs4 parents: diff changeset	90
60609a9cef3b Uploaded crs4 parents: diff changeset	91 This tool uses `Edena`_, which is licensed separately. Please cite \|Hernandez2008\|_.
60609a9cef3b Uploaded crs4 parents: diff changeset	92
60609a9cef3b Uploaded crs4 parents: diff changeset	93 .. _Edena: http://www.genomic.ch/edena.php
60609a9cef3b Uploaded crs4 parents: diff changeset	94 .. \|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	95 .. _Hernandez2008: http://genome.cshlp.org/content/18/5/802
60609a9cef3b Uploaded crs4 parents: diff changeset	96 </help>
60609a9cef3b Uploaded crs4 parents: diff changeset	97 </tool>

Mercurial > repos > crs4 > edena

annotate edena_ass_wrapper.xml @ 2:b8c6a38530eb draft default tip