oasesoptimiser: oases_optimiser.xml annotate

annotate oases_optimiser.xml @ 0:d35f713f5dc4 default tip

Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository

author	konradpaszkiewicz
date	Tue, 07 Jun 2011 17:09:27 -0400
parents
children

rev	line source
0 d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	1 <tool id="oasesoptimiser" name="oasesoptimiser" version="1.0.0">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	2 <description>Auto optimise a denovo RNA-seq Oases/Velvet assembly</description>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	3 <command interpreter="python">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	4 oases_optimiser.py '$start_hash_length' '$end_hash_length'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	5 '#for $i in $inputs
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	6 ${i.file_format}
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	7 ${i.read_type}
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	8 ${i.input}
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	9 #end for
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	10 '
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	11 '$contigs'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	12 '$LastGraph'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	13 '$velvet_asm'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	14 '$unused_reads_fasta'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	15 '$stats'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	16 '$othervelvetgoptions'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	17 '$otheroasesoptions'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	18 '$transcripts'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	19 '$splicingevents'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	20 '$contigordering'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	21 '$contigs.extra_files_path'
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	22 </command>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	23
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	24 <inputs>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	25 <param label="Start Hash Length" name="start_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Shorter hash lengths (i.e. less than 31) may cause out-of-memory problems.">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	26
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	27 <option value="23">23</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	28 <option value="25">25</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	29 <option value="27">27</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	30 <option value="29">29</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	31 <option value="31" selected="yes">31</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	32 <option value="33">33</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	33 <option value="35">35</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	34 <option value="37">37</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	35 <option value="39">39</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	36 <option value="41">41</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	37
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	38 </param>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	39 <param label="End Hash Length" name="end_hash_length" type="select" help="k-mer length in base pairs of the words being hashed.">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	40 <option value="43">43</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	41 <option value="45">45</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	42 <option value="47">47</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	43 <option value="49">49</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	44 <option value="51">51</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	45 <option value="53">53</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	46 <option value="55">55</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	47 <option value="57">57</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	48 <option value="59">59</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	49 <option value="61">61</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	50 <option value="63">63</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	51 <option value="65">65</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	52 <option value="67">67</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	53 <option value="69" selected="yes">69</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	54
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	55 </param>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	56
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	57
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	58 <param label="Advanced velvetg options" name="othervelvetgoptions" title="Advanced velvetg options" help="Other Velvetg options - see below for details" type="text" size="30">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	59
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	60 </param>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	61
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	62
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	63 <param label="Advanced Oases options" default="-ins_length 50 -ins_length_sd 100" name="otheroasesoptions" title="Advanced oases options" help="Other oases options - see below for details" type="text" size="30">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	64
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	65 </param>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	66
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	67 <param name="strand_specific" type="boolean" checked="false" truevalue="-strand_specific" falsevalue="" label="Use strand specific transcriptome sequencing" help="If you are using a strand specific transcriptome sequencing protocol, you may wish to use this option for better results."/>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	68 <repeat name="inputs" title="Input Files">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	69 <param label="file format" name="file_format" type="select">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	70 <option value="-fasta" selected="yes">fasta</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	71 <option value="-fastq">fastq</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	72 <option value="-eland">eland</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	73 <option value="-gerald">gerald</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	74 </param>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	75 <param label="read type" name="read_type" type="select">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	76 <option value="-short" selected="yes">short reads</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	77 <option value="-shortPaired">shortPaired reads</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	78 <option value="-short2">short2 reads</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	79 <option value="-shortPaired2">shortPaired2 reads</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	80 <option value="-long">long reads (reads >200bp e.g. 454 reads)</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	81 <option value="-longPaired">longPaired reads</option>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	82 </param>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	83
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	84
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	85 <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	86 </repeat>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	87 </inputs>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	88
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	89 <outputs>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	90
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	91 <data format="fasta" name="transcripts" label="${tool.name} on ${on_string}: Denovo assembled transcripts"/>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	92 <data format="tabular" name="splicingevents" label="${tool.name} on ${on_string}: Splicing events in assembled transcripts"/>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	93 <data format="tabular" name="contigordering" label="${tool.name} on ${on_string}: Contig ordering in assembled transcripts"/>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	94 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Denovo assembled contigs"/>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	95
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	96 <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	97 <!-- <filter>unused_reads['generate_unused'] == "yes"</filter>-->
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	98 </data>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	99 <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats"/>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	100 <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	101 <!-- <filter>generate_amos['afg'] == "yes"</filter> -->
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	102 </data>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	103
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	104 <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph">
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	105 <!-- <filter>last_graph['generate_graph'] == "yes"</filter> -->
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	106 </data>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	107
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	108
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	109 </outputs>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	110 <requirements>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	111 <requirement type="package">velvet</requirement>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	112 <requirement type="package">oases</requirement>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	113
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	114 </requirements>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	115
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	116 <help>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	117 Oases Optimiser Overview
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	118
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	119 Oases_ is a de novo transcriptome assembler specially designed to work with short reads. It is an extension of Velvet developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	120
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	121 Provide all the information about insert lengths and their standard deviation as
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	122 possible (identical to Velvet). In the advanced oases options you should set the -ins_length flag when using paired-end reads (e.g. -ins_length 200 -ins_length_sd 100). If you do not do this, then paired-end information will not be used by Oases!
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	123
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	124 ----------------------------------------------------------------------------------
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	125
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	126 Oases produces a number of output files, which correspond to the different algorithms
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	127 being run succesively on the data. In the above example, you would find:
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	128
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	129 transcripts.fa
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	130 A FASTA file containing the transcripts imputed directly from trivial
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	131 clusters of contigs (loci with less than two transcripts and Confidence Values = 1)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	132 and the highly expressed transcripts imputed by dynamic
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	133 programming (loci with more than 2 transcripts and Confidence Values less than 1).
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	134
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	135 splicing_events.txt
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	136 A hybrid file which describes the contigs contained in each locus in FASTA
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	137 format, interlaced with one line descriptions of splicing events using the
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	138 AStalavista nomenclature*.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	139
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	140 Read the Oases `documentation`__ for details on using the Oases Assembler.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	141
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	142 .. _Velvet: http://www.ebi.ac.uk/~zerbino/oases/
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	143
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	144 .. __: http://www.ebi.ac.uk/~zerbino/oases/Manual.txt
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	145
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	146 ------
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	147
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	148 Other outputs (as per Velvet)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	149
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	150
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	151 Contigs
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	152
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	153 The contigs.fa file.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	154 This fasta file contains the sequences of the contigs longer than 2k, where k is the word-length used in velveth. If you have specified a min contig lgth threshold, then the contigs shorter than that value are omitted.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	155 Note that the length and coverage information provided in the header of each contig should therefore be understood in k-mers and in k-mer coverage (cf. 5.1) respectively.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	156 The N's in the sequence correspond to gaps between scaffolded contigs. The number of N's corresponds to the estimated length of the gap. For reasons of compatibility with the archives, any gap shorter than 10bp is represented by a sequence of 10 N's.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	157
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	158 Stats
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	159
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	160 The stats.txt file.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	161 This file is a simple tabbed-delimited description of the nodes. The column names are pretty much self-explanatory. Note however that node lengths are given in k-mers. To obtain the length in nucleotides of each node you simply need to add k - 1, where k is the word-length used in velveth.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	162 The in and out columns correspond to the number of arcs on the 5' and 3' ends of the contig respectively.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	163 The coverages in columns short1 cov, short1 Ocov, short2 cov, and short2 Ocov are provided in k-mer coverage (5.1).
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	164 Also, the difference between # cov and # Ocov is the way these values are computed. In the first count, slightly divergent sequences are added to the coverage tally. However, in the second, stricter count, only the sequences which map perfectly onto the consensus sequence are taken into account.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	165
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	166 LastGraph
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	167
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	168 The LastGraph file.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	169 This file describes in its entirety the graph produced by Velvet.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	170
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	171 AMOS.afg
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	172 The velvet_asm.afg file.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	173 This file is mainly designed to be read by the open-source AMOS genome assembly package. Nonetheless, a number of programs are available to transform this kind of file into other assembly file formats (namely ACE, TIGR, Arachne and Celera). See http://amos.sourceforge.net/ for more information.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	174 The file describes all the contigs contained in the contigs.fa file (cf 4.2.1).
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	175
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	176 Advanced options
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	177 -ins_length integer : expected distance between two paired-end reads in the first short-read dataset (default: no read pairing)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	178 -ins_length2 integer : expected distance between two paired-end reads in the second short-read dataset (default: no read pairing)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	179 -ins_length_long integer : expected distance between two long paired-end reads (default: no read pairing)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	180 -ins_length*_sd integer : est. standard deviation of respective dataset (default: 10% of corresponding length)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	181 -scaffolding yes\|no : scaffolding of contigs used paired end information (default: on)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	182 -max_branch_length integer : maximum length in base pair of bubble (default: 100)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	183 -max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	184 -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	185 -min_pair_count integer : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	186 -max_coverage floating point : removal of high coverage nodes AFTER tour bus (default: no removal)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	187 -long_mult_cutoff int : minimum number of long reads required to merge contigs (default: 2)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	188 -min_trans_length
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	189 simple threshold on output transcript length
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	190 -cov_cutoff
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	191 minimum number of times a k-mer has to be observed to be used in the
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	192 assembly (just like in Velvet) [default=3]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	193 -min_pair_cov
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	194 minimum number of times two contigs must be connected by reads or read pairs to be clustered together [default=4]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	195 -paired_cutoff
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	196 minimum ratio between the numbers of observed and expected connecting
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	197 read pairs between two contigs [default=0.1]
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	198
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	199
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	200
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	201 Hash Length
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	202
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	203 The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	204
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	205 The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	206
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	207 # it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	208 # it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	209 # it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	210
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	211 Now you still have quite a lot of possibilities. As is often the case, it's a trade- off between specificity and sensitivity. Longer kmers bring you more specificity (i.e. less spurious overlaps) but lowers coverage (cf. below). . . so there's a sweet spot to be found with time and experience.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	212 We like to think in terms of "k-mer coverage", i.e. how many times has a k-mer been seen among the reads. The relation between k-mer coverage Ck and standard (nucleotide-wise) coverage C is Ck = C # (L - k + 1)/L where k is your hash length, and L you read length.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	213 Experience shows that this kmer coverage should be above 10 to start getting decent results. If Ck is above 20, you might be "wasting" coverage. Experience also shows that empirical tests with different values for k are not that costly to run! VelvetOptimiser automates these tests for you.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	214
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	215
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	216 Velvetg options
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	217
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	218
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	219
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	220 Input Files
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	221
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	222 Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	223 read. In other words, if the reads are indexed from 0, then reads 0 and 1 are paired, 2 and 3, 4 and 5, etc.
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	224
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	225 Supported file formats are::
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	226
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	227 fasta
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	228 fastq
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	229 eland
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	230 gerald
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	231
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	232 Read categories are::
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	233
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	234 short (default)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	235 shortPaired
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	236 short2 (same as short, but for a separate insert-size library - i.e. if you have two libraries of different lengths)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	237 shortPaired2 (see above)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	238 long (for Sanger, 454 or even reference sequences)
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	239 longPaired
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	240
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	241 </help>
d35f713f5dc4 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository konradpaszkiewicz parents: diff changeset	242 </tool>

Mercurial > repos > konradpaszkiewicz > oasesoptimiser

annotate oases_optimiser.xml @ 0:d35f713f5dc4 default tip