edena: edena_ovl_wrapper.xml annotate

annotate edena_ovl_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_ovl_wrapper" name="Edena (overlapping)" 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
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	9 -nThreads \${GALAXY_SLOTS:-2}
0 60609a9cef3b Uploaded crs4 parents: diff changeset	10 #if $input_selection.input == "unpaired_file"
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	11 -r
1 cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	12 #for $ui in $input_selection.unpaired_input
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 ${ui.unpaired_file}
0 60609a9cef3b Uploaded crs4 parents: diff changeset	14 #end for
60609a9cef3b Uploaded crs4 parents: diff changeset	15 #elif $input_selection.input == "dr_pairs"
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	16 -DRpairs
1 cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	17 #for $dpi in $input_selection.dr_pairs_input
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 ${dpi.dr_pair_1} ${dpi.dr_pair_2}
0 60609a9cef3b Uploaded crs4 parents: diff changeset	19 #end for
60609a9cef3b Uploaded crs4 parents: diff changeset	20 #elif $input_selection.input == "rd_pairs"
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	21 -RDpairs
1 cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	22 #for $rpi in $input_selection.rd_pairs_input
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 ${rpi.rd_pair_1} ${rpi.rd_pair_2}
0 60609a9cef3b Uploaded crs4 parents: diff changeset	24 #end for
60609a9cef3b Uploaded crs4 parents: diff changeset	25 #end if
60609a9cef3b Uploaded crs4 parents: diff changeset	26 #if str($minOlap)
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	27 -M $minOlap
0 60609a9cef3b Uploaded crs4 parents: diff changeset	28 #end if
60609a9cef3b Uploaded crs4 parents: diff changeset	29 #if str($readsTruncation)
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	30 -t $readsTruncation
0 60609a9cef3b Uploaded crs4 parents: diff changeset	31 #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	32 2>/dev/null ## need to discard stderr because edena writes some progress info there (e.g. "Computing overlaps >=30...")
0 60609a9cef3b Uploaded crs4 parents: diff changeset	33 </command>
60609a9cef3b Uploaded crs4 parents: diff changeset	34
60609a9cef3b Uploaded crs4 parents: diff changeset	35 <inputs>
60609a9cef3b Uploaded crs4 parents: diff changeset	36 <conditional name="input_selection">
60609a9cef3b Uploaded crs4 parents: diff changeset	37 <param name="input" type="select" label="Select input type">
1 cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	38 <option value="unpaired_file">Unpaired files</option>
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	39 <option value="dr_pairs">Paired-end (forward-reverse) files</option>
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	40 <option value="rd_pairs">Mate-pair (reverse-forward) files</option>
0 60609a9cef3b Uploaded crs4 parents: diff changeset	41 </param>
60609a9cef3b Uploaded crs4 parents: diff changeset	42
60609a9cef3b Uploaded crs4 parents: diff changeset	43 <when value="unpaired_file">
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	44 <repeat name="unpaired_input" title="Unpaired input" help="(-r)" min="1">
0 60609a9cef3b Uploaded crs4 parents: diff changeset	45 <param name="unpaired_file" type="data" format="fasta,fastq" label="Unpaired file" help="FASTA or FASTQ format" />
60609a9cef3b Uploaded crs4 parents: diff changeset	46 </repeat>
60609a9cef3b Uploaded crs4 parents: diff changeset	47 </when>
60609a9cef3b Uploaded crs4 parents: diff changeset	48
60609a9cef3b Uploaded crs4 parents: diff changeset	49 <when value="dr_pairs">
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	50 <repeat name="dr_pairs_input" title="Paired-end (forward-reverse) file" help="(-DRpairs, -paired)" min="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	51 <param name="dr_pair_1" type="data" format="fasta,fastq" label="Paired-end file 1" help="FASTA or FASTQ format" />
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	52 <param name="dr_pair_2" type="data" format="fasta,fastq" label="Paired-end file 2" help="FASTA or FASTQ format" />
0 60609a9cef3b Uploaded crs4 parents: diff changeset	53 </repeat>
60609a9cef3b Uploaded crs4 parents: diff changeset	54 </when>
60609a9cef3b Uploaded crs4 parents: diff changeset	55
60609a9cef3b Uploaded crs4 parents: diff changeset	56 <when value="rd_pairs">
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	57 <repeat name="rd_pairs_input" title="Mate-pair (reverse-forward) file" help="(-RDpairs, -matePairs)" min="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	58 <param name="rd_pair_1" type="data" format="fasta,fastq" label="Mate-pair file 1" help="FASTA or FASTQ format" />
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 <param name="rd_pair_2" type="data" format="fasta,fastq" label="Mate-pair file 2" help="FASTA or FASTQ format" />
0 60609a9cef3b Uploaded crs4 parents: diff changeset	60 </repeat>
60609a9cef3b Uploaded crs4 parents: diff changeset	61 </when>
60609a9cef3b Uploaded crs4 parents: diff changeset	62 </conditional>
60609a9cef3b Uploaded crs4 parents: diff changeset	63
60609a9cef3b Uploaded crs4 parents: diff changeset	64 <param name="minOlap" type="integer" value="" optional="true" label="Minimum overlap size to compute (-M)" help="If not specified, this value is set to half of the reads length. When the sequencing coverage is sufficient, you can increase this value which will reduce the computational time. Edena will compute the overlaps whose sizes range from this value to the reads length." />
60609a9cef3b Uploaded crs4 parents: diff changeset	65
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	66 <param name="readsTruncation" type="integer" value="" optional="true" label="3' end reads truncation (-t)" help="Use this option to truncate the 3’end of the reads to the specified length. You may consider reads truncation since it can significantly improve the assembly. Since Edena computes exact overlaps, only error free reads can take part to the assembly. Since errors are likely to occur at the 3’ ends, shortening the reads by some nucleotides may increase the number of errors-free reads in the dataset, and thus increase the assembly performance." />
0 60609a9cef3b Uploaded crs4 parents: diff changeset	67
60609a9cef3b Uploaded crs4 parents: diff changeset	68 </inputs>
60609a9cef3b Uploaded crs4 parents: diff changeset	69
60609a9cef3b Uploaded crs4 parents: diff changeset	70 <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 $EDENA crs4 parents: 1 diff changeset	71 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="out_overlapping.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 $EDENA crs4 parents: 1 diff changeset	72 <data name="output" format="ovl" label="${tool.name} on ${on_string}: overlapping" from_work_dir="out.ovl" />
0 60609a9cef3b Uploaded crs4 parents: diff changeset	73 </outputs>
60609a9cef3b Uploaded crs4 parents: diff changeset	74
60609a9cef3b Uploaded crs4 parents: diff changeset	75 <tests>
60609a9cef3b Uploaded crs4 parents: diff changeset	76
60609a9cef3b Uploaded crs4 parents: diff changeset	77 </tests>
60609a9cef3b Uploaded crs4 parents: diff changeset	78 <help>
60609a9cef3b Uploaded crs4 parents: diff changeset	79 What it does
60609a9cef3b Uploaded crs4 parents: diff changeset	80
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	81 Edena is an overlaps graph based short reads assembler and is suited to Illumina GA reads. This program requires the reads to be all the same length, as Illumina GA reads are. This is due to historical reasons and because it greatly simplifies several computational steps. 454 or Sanger reads are therefore not suited to Edena. If you provide multiple files with different read lengths, Edena will trim the 3’ end of the reads so that the reads are all the same length as the shortest reads in the file.
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	82
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	83 An assembly with Edena is a two step process: overlapping and assembling.
1 cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	84
cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	85 In the overlapping step, the reads files are provided to the program which computes the transitively reduced overlaps graph. This structure is then stored together with the sequence reads in the overlapping file.
cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	86
cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	87 Edena can accept both unpaired and paired files, FASTQ and FASTA format. Note that for technical reasons, all reads are required to be of the same length. You can however provide the program with different files containing different reads length. In such case, Edena will trim the 3’ ends of the longer reads so that they fit the shorter length. It is however required that reads within each individual file are of the same length (as Illumina GA reads are). By default all overlaps with a minimum size corresponding to half of the reads length are computed. This is quite conservative. Provided enough coverage, this value can be increased (option -M) to reduce the memory requirements.
cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	88
cd6cc6d76708 Simplify passing repeated params to Python script. crs4 parents: 0 diff changeset	89 For reads longer than 100bp, you may consider the reads truncation option, which could help in discarding 3’ base calling errors.
0 60609a9cef3b Uploaded crs4 parents: diff changeset	90
60609a9cef3b Uploaded crs4 parents: diff changeset	91 License and citation
60609a9cef3b Uploaded crs4 parents: diff changeset	92
60609a9cef3b Uploaded crs4 parents: diff changeset	93 This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_.
60609a9cef3b Uploaded crs4 parents: diff changeset	94
60609a9cef3b Uploaded crs4 parents: diff changeset	95 .. _CRS4 Srl.: http://www.crs4.it/
60609a9cef3b Uploaded crs4 parents: diff changeset	96 .. _MIT license: http://opensource.org/licenses/MIT
60609a9cef3b Uploaded crs4 parents: diff changeset	97
60609a9cef3b Uploaded crs4 parents: diff changeset	98 If you use this tool in Galaxy, please cite \|Cuccuru2013\|_.
60609a9cef3b Uploaded crs4 parents: diff changeset	99
60609a9cef3b Uploaded crs4 parents: diff changeset	100 .. \|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	101 .. _Cuccuru2013: http://orione.crs4.it/
60609a9cef3b Uploaded crs4 parents: diff changeset	102
60609a9cef3b Uploaded crs4 parents: diff changeset	103 This tool uses `Edena`_, which is licensed separately. Please cite \|Hernandez2008\|_.
60609a9cef3b Uploaded crs4 parents: diff changeset	104
60609a9cef3b Uploaded crs4 parents: diff changeset	105 .. _Edena: http://www.genomic.ch/edena.php
60609a9cef3b Uploaded crs4 parents: diff changeset	106 .. \|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	107 .. _Hernandez2008: http://genome.cshlp.org/content/18/5/802
60609a9cef3b Uploaded crs4 parents: diff changeset	108 </help>
60609a9cef3b Uploaded crs4 parents: diff changeset	109 </tool>

Mercurial > repos > crs4 > edena

annotate edena_ovl_wrapper.xml @ 2:b8c6a38530eb draft default tip