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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_oases commit 47a8a06faad1aa3c36503934ee2fd9e6031d3b75
author drosofff
date Thu, 12 May 2016 10:45:03 -0400
parents f08d9c814ffb
children 68ed36eed6c5
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3:f08d9c814ffb 4:dc684e37f668
1 <tool id="oasesoptimiserv" name="Oases_optimiser" version="1.1.4"> 1 <tool id="oasesoptimiserv" name="Oases_optimiser" version="1.1.5">
2 <description>Auto optimise de novo RNA-seq Oases/Velvet assembly</description> 2 <description>Auto optimise de novo RNA-seq Oases/Velvet assembly</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.08_7a32460a60929b510037952ae815bb6e29b68123">oases</requirement> 4 <requirement type="package" version="0.2.08_7a32460a60929b510037952ae815bb6e29b68123">oases</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command><![CDATA[
7 oases_optimiser.py '$start_hash_length' '$end_hash_length' 7 python "$__tool_directory__"/oases_optimiser.py "$start_hash_length" "$end_hash_length"
8 '#for $i in $inputs 8 #for $i in $inputs
9 ${i.input} 9 "${i.input}"
10 #end for 10 #end for
11 ' 11 "$transcripts"
12 '$transcripts' 12 ]]></command>
13 </command> 13 <inputs>
14 14 <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.">
15 <inputs> 15 <option value="11" selected="yes">11</option>
16 <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."> 16 <option value="13">13</option>
17 <option value="11" selected="yes">11</option> 17 <option value="15">15</option>
18 <option value="13">13</option> 18 <option value="17">17</option>
19 <option value="15">15</option> 19 <option value="19">19</option>
20 <option value="17">17</option> 20 <option value="21">21</option>
21 <option value="19">19</option> 21 <option value="23">23</option>
22 <option value="21">21</option> 22 <option value="25">25</option>
23 <option value="23">23</option> 23 <option value="35">35</option>
24 <option value="25">25</option> 24 <option value="45">45</option>
25 <option value="35">35</option> 25 <option value="55">55</option>
26 <option value="45">45</option> 26 <option value="65">65</option>
27 <option value="55">55</option> 27 </param>
28 <option value="65">65</option> 28 <param label="End Hash Length" name="end_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Value has to be higher than the Start Hash Length value">
29 </param> 29 <option value="25">25</option>
30 <param label="End Hash Length" name="end_hash_length" type="select" help="k-mer length in base pairs of the words being hashed. Value has to be higher than the Start Hash Length value"> 30 <option value="27">27</option>
31 <option value="25">25</option> 31 <option value="29">29</option>
32 <option value="27">27</option> 32 <option value="31">31</option>
33 <option value="29">29</option> 33 <option value="33">33</option>
34 <option value="31">31</option> 34 <option value="35">35</option>
35 <option value="33">33</option> 35 <option value="45">45</option>
36 <option value="35">35</option> 36 <option value="55">55</option>
37 <option value="45">45</option> 37 <option value="63">63</option>
38 <option value="55">55</option> 38 <option value="69">69</option>
39 <option value="63">63</option> 39 </param>
40 <option value="69">69</option> 40 <repeat name="inputs" title="Input Files">
41 </param> 41 <param name="input" type="data" format="fasta" label="Dataset: short reads, fasta format"/>
42 42 </repeat>
43 43 </inputs>
44 44 <outputs>
45 <repeat name="inputs" title="Input Files">
46 <param name="input" type="data" format="fasta" label="Dataset: short reads, fasta format"/>
47 </repeat>
48 </inputs>
49
50 <outputs>
51 <data format="fasta" name="transcripts" label="${tool.name} on ${on_string}: Denovo assembled transcripts"/> 45 <data format="fasta" name="transcripts" label="${tool.name} on ${on_string}: Denovo assembled transcripts"/>
52 </outputs> 46 </outputs>
53 <tests> 47 <tests>
54 <test> 48 <test>
55 <param name="input" value="input.fa" ftype="fasta"/> 49 <param name="input" value="input.fa" ftype="fasta"/>
56 <param name="start_hash_length" value="15" /> 50 <param name="start_hash_length" value="15" />
57 <param name="end_hash_length" value="35" /> 51 <param name="end_hash_length" value="35" />
58 <output name="transcripts" file="output.fa"/> 52 <output name="transcripts" file="output.fa"/>
59 </test> 53 </test>
60 </tests> 54 </tests>
61
62 <help> 55 <help>
63 **Oases Optimiser Overview** 56 **Oases Optimiser Overview**
64 57
65 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. 58 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.
66 59
83 format, interlaced with one line descriptions of splicing events using the 76 format, interlaced with one line descriptions of splicing events using the
84 AStalavista nomenclature*. 77 AStalavista nomenclature*.
85 78
86 Read the Oases `documentation`__ for details on using the Oases Assembler. 79 Read the Oases `documentation`__ for details on using the Oases Assembler.
87 80
88 .. _Velvet: http://www.ebi.ac.uk/~zerbino/oases/ 81 .. _Oases: http://www.ebi.ac.uk/~zerbino/oases/
89 82
90 .. __: http://www.ebi.ac.uk/~zerbino/oases/Manual.txt 83 .. __: http://www.ebi.ac.uk/~zerbino/oases/Manual.txt
91 84
92 ------ 85 ------
93 86
118 The *velvet_asm.afg* file. 111 The *velvet_asm.afg* file.
119 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. 112 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.
120 The file describes all the contigs contained in the contigs.fa file (cf 4.2.1). 113 The file describes all the contigs contained in the contigs.fa file (cf 4.2.1).
121 114
122 **Advanced options** 115 **Advanced options**
123 -ins_length integer : expected distance between two paired-end reads in the first short-read dataset (default: no read pairing) 116 -ins_length integer: expected distance between two paired-end reads in the first short-read dataset (default: no read pairing)
124 -ins_length2 integer : expected distance between two paired-end reads in the second short-read dataset (default: no read pairing) 117 -ins_length2 integer: expected distance between two paired-end reads in the second short-read dataset (default: no read pairing)
125 -ins_length_long integer : expected distance between two long paired-end reads (default: no read pairing) 118 -ins_length_long integer: expected distance between two long paired-end reads (default: no read pairing)
126 -ins_length*_sd integer : est. standard deviation of respective dataset (default: 10% of corresponding length) 119 -ins_length_sd integer: est. standard deviation of respective dataset (default: 10% of corresponding length)
127 -scaffolding yes|no : scaffolding of contigs used paired end information (default: on) 120 -scaffolding yes|no: scaffolding of contigs used paired end information (default: on)
128 -max_branch_length integer : maximum length in base pair of bubble (default: 100) 121 -max_branch_length integer: maximum length in base pair of bubble (default: 100)
129 -max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2) 122 -max_divergence floating-point: maximum divergence rate between two branches in a bubble (default: 0.2)
130 -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3) 123 -max_gap_count integer: maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
131 -min_pair_count integer : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10) 124 -min_pair_count integer: minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)
132 -max_coverage floating point : removal of high coverage nodes AFTER tour bus (default: no removal) 125 -max_coverage floating point: removal of high coverage nodes AFTER tour bus (default: no removal)
133 -long_mult_cutoff int : minimum number of long reads required to merge contigs (default: 2) 126 -long_mult_cutoff int: minimum number of long reads required to merge contigs (default: 2)
134 -min_trans_length 127 -min_trans_length: simple threshold on output transcript length
135 simple threshold on output transcript length 128 -cov_cutoff: minimum number of times a k-mer has to be observed to be used in the assembly (just like in Velvet) [default=3]
136 -cov_cutoff 129 -min_pair_cov: minimum number of times two contigs must be connected by reads or read pairs to be clustered together [default=4]
137 minimum number of times a k-mer has to be observed to be used in the 130 -paired_cutoff: minimum ratio between the numbers of observed and expected connecting read pairs between two contigs [default=0.1]
138 assembly (just like in Velvet) [default=3]
139 -min_pair_cov
140 minimum number of times two contigs must be connected by reads or read pairs to be clustered together [default=4]
141 -paired_cutoff
142 minimum ratio between the numbers of observed and expected connecting
143 read pairs between two contigs [default=0.1]
144
145 131
146 132
147 **Hash Length** 133 **Hash Length**
148 134
149 The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed. 135 The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.
155 # it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons. 141 # it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.
156 142
157 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. 143 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.
158 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. 144 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.
159 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. 145 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.
146 Occasionally oases crashes at specific k-mers, in that case this Galaxy wrapper will skip this k-mer and continue the analysis without this k-mer.
160 147
161 148
162 **Velvetg options** 149 **Velvetg options**
163 150
164 151
173 160
174 Read categories are:: 161 Read categories are::
175 162
176 short (default) 163 short (default)
177 164
178 </help> 165 </help>
166 <citations>
167 <citation type="doi">10.1093/bioinformatics/bts094</citation>
168 <citation type="doi">10.1101/gr.074492.107</citation>
169 </citations>
179 </tool> 170 </tool>