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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/oases commit d5a2de4b4c556e028fc5ef7ffcc7c2d0cf31c5ec
author artbio
date Mon, 12 Feb 2024 23:55:39 +0000
parents c9b5ec6c45e8
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1:c9b5ec6c45e8 2:ab37eb09b4ca
1 <tool id="oasesoptimiserv" name="Oases_optimiser" version="1.3.0"> 1 <tool id="oasesoptimiserv" name="Oases_optimiser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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 <macros>
4 <token name="@TOOL_VERSION@">1.4.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 <token name="@PROFILE@">23.0</token>
7 </macros>
3 <requirements> 8 <requirements>
4 <requirement type="package" version="0.2.09">oases</requirement> 9 <requirement type="package" version="0.2.09">oases</requirement>
5 <requirement type="package" version="1.2.10">velvet</requirement> 10 <requirement type="package" version="1.2.10">velvet</requirement>
6 <requirement type="package" version="3.7.6">python</requirement> 11 <requirement type="package" version="3.12.1">python</requirement>
7 </requirements> 12 </requirements>
8 <command><![CDATA[ 13 <command><![CDATA[
9 python "$__tool_directory__"/oases_optimiser.py "$start_hash_length" "$end_hash_length" 14 python '$__tool_directory__/oases_optimiser.py' '$start_hash_length' '$end_hash_length'
10 #for $i in $inputs 15 #for $i in $inputs
11 "${i.input}" 16 '${i.input}'
12 #end for 17 #end for
13 "$transcripts" 18 '$transcripts'
14 ]]></command> 19 ]]></command>
15 <inputs> 20 <inputs>
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."> 21 <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.">
17 <option value="11" selected="yes">11</option> 22 <option value="11" selected="yes">11</option>
18 <option value="13">13</option> 23 <option value="13">13</option>
19 <option value="15">15</option> 24 <option value="15">15</option>
57 <has_line_matching expression=">Locus_25_Transcript_1/1_Confidence_.+" /> 62 <has_line_matching expression=">Locus_25_Transcript_1/1_Confidence_.+" />
58 </assert_contents> 63 </assert_contents>
59 </output> 64 </output>
60 </test> 65 </test>
61 </tests> 66 </tests>
62 <help> 67 <help>
63 **Oases Optimiser Overview** 68 **Oases Optimiser Overview**
64 69
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. 70 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 71
67 Provide all the information about insert lengths and their standard deviation as 72 Provide all the information about insert lengths and their standard deviation as
71 76
72 Oases produces a number of output files, which correspond to the different algorithms 77 Oases produces a number of output files, which correspond to the different algorithms
73 being run succesively on the data. In the above example, you would find: 78 being run succesively on the data. In the above example, you would find:
74 79
75 transcripts.fa 80 transcripts.fa
76 A FASTA file containing the transcripts imputed directly from trivial 81 A FASTA file containing the transcripts imputed directly from trivial
77 clusters of contigs (loci with less than two transcripts and Confidence Values = 1) 82 clusters of contigs (loci with less than two transcripts and Confidence Values = 1)
78 and the highly expressed transcripts imputed by dynamic 83 and the highly expressed transcripts imputed by dynamic
79 programming (loci with more than 2 transcripts and Confidence Values less than 1). 84 programming (loci with more than 2 transcripts and Confidence Values less than 1).
80 85
81 splicing_events.txt 86 splicing_events.txt
82 A hybrid file which describes the contigs contained in each locus in FASTA 87 A hybrid file which describes the contigs contained in each locus in FASTA
83 format, interlaced with one line descriptions of splicing events using the 88 format, interlaced with one line descriptions of splicing events using the
84 AStalavista nomenclature*. 89 AStalavista nomenclature*.
85 90
86 Read the Oases `documentation`__ for details on using the Oases Assembler. 91 Read the Oases `documentation`__ for details on using the Oases Assembler.
87 92
88 .. _Oases: http://www.ebi.ac.uk/~zerbino/oases/ 93 .. _Oases: https://github.com/dzerbino/oases
89 94
90 .. __: http://www.ebi.ac.uk/~zerbino/oases/Manual.txt 95 .. __: https://bioweb.pasteur.fr/docs/modules/oases/0.2.08/OasesManual.pdf
91 96
92 ------ 97 ------
93 98
94 **Other outputs (as per Velvet)** 99 **Other outputs (as per Velvet)**
95 100