Mercurial > repos > devteam > velvet

annotate velveth.xml @ 0:c170448acc8a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:02:53 -0500
parents
children c397035f715d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
1 <tool id="velveth" name="velveth" version="@WRAPPER_VERSION@.0">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
2 <description>Prepare a dataset for the Velvet velvetg Assembler</description>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
3 <version_command>velveth 2&gt;&amp;1 | grep "Version" | sed -e 's/Version //'</version_command>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
4 <macros>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
5 <import>macros.xml</import>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
6 </macros>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
7 <expand macro="requirements"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
8 <expand macro="stdio"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
9 <command interpreter="python">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
10 velveth_wrapper.py
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
11 '$out_file1' '$out_file1.extra_files_path'
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
12 $hash_length
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
13 $strand_specific
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
14 #for $i in $inputs
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
15 ${i.file_format}
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
16 ${i.read_type}
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
17 ${i.input}
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
18 #end for
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
19 </command>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
20 <inputs>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
21 <param label="Hash Length" name="hash_length" type="select" help="k-mer length in base pairs of the words being hashed.">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
22 <option value="11">11</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
23 <option value="13">13</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
24 <option value="15">15</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
25 <option value="17">17</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
26 <option value="19">19</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
27 <option value="21" selected="yes">21</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
28 <option value="23">23</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
29 <option value="25">25</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
30 <option value="27">27</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
31 <option value="29">29</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
32 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
33 <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."/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
34 <repeat name="inputs" title="Input Files">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
35 <param label="file format" name="file_format" type="select">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
36 <option value="-fasta" selected="yes">fasta</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
37 <option value="-fastq">fastq</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
38 <option value="-eland">eland</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
39 <option value="-gerald">gerald</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
40 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
41 <param label="read type" name="read_type" type="select">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
42 <option value="-short" selected="yes">short reads</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
43 <option value="-shortPaired">shortPaired reads</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
44 <option value="-short2">short2 reads</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
45 <option value="-shortPaired2">shortPaired2 reads</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
46 <option value="-long">long reads</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
47 <option value="-longPaired">longPaired reads</option>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
48 </param>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
49
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
50 <param name="input" type="data" format="fasta,fastq,eland,gerald" label="Dataset"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
51 </repeat>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
52 </inputs>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
53 <outputs>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
54 <data format="velvet" name="out_file1" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
55 </outputs>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
56 <requirements>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
57 <requirement type="package">velvet</requirement>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
58 </requirements>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
59 <tests>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
60 <test>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
61 <param name="hash_length" value="21" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
62 <param name="read_type" value="-shortPaired" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
63 <!-- <repeat name="inputs"> -->
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
64 <param name="file_format" value="fasta" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
65 <param name="read_type" value="shortPaired reads" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
66 <param name="input" value="velvet_test_reads.fa" ftype="fasta" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
67 <!-- </repeat> -->
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
68 <param name="strand_specific" value="" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
69 <output name="out_file1" file="velveth_test1/output.html" lines_diff="4">
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
70 <extra_files type="file" name='Sequences' value="velveth_test1/Sequences" compare="diff" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
71 <extra_files type="file" name='Roadmaps' value="velveth_test1/Roadmaps" compare="diff" />
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
72 </output>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
73 </test>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
74 </tests>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
75 <help>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
76
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
77 **What it does**
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
78
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
79 Velvet_ is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
80
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
81 Velvet currently takes in short read sequences, removes errors then produces high quality unique contigs. It then uses paired-end read and long read information, when available, to retrieve the repeated areas between contigs.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
82
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
83 Read the Velvet `documentation`__ for details on using the Velvet Assembler.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
84
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
85 .. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
86
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
87 .. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
88
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
89 ------
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
90
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
91 **Velveth**
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
92
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
93 Velveth takes in a number of sequence files, produces a hashtable, then outputs two files in an output directory (creating it if necessary), Sequences and Roadmaps, which are necessary to velvetg.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
94
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
95 ------
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
96
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
97 **Hash Length**
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
98
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
99 The hash length, also known as k-mer length, corresponds to the length, in base pairs, of the words being hashed.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
100
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
101 The hash length is the length of the k-mers being entered in the hash table. Firstly, you must observe three technical constraints::
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
102
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
103 # it must be an odd number, to avoid palindromes. If you put in an even number, Velvet will just decrement it and proceed.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
104 # it must be below or equal to MAXKMERHASH length (cf. 2.3.3, by default 31bp), because it is stored on 64 bits
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
105 # it must be strictly inferior to read length, otherwise you simply will not observe any overlaps between reads, for obvious reasons.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
106
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
107 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.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
108 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.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
109 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!
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
110
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
111 **Input Files**
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
112
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
113 Velvet works mainly with fasta and fastq formats. For paired-end reads, the assumption is that each read is next to its mate
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
114 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.
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
115
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
116 Supported file formats are::
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
117
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
118 fasta
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
119 fastq
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
120 fasta.gz
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
121 fastq.gz
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
122 eland
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
123 gerald
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
124
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
125 Read categories are::
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
126
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
127 short (default)
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
128 shortPaired
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
129 short2 (same as short, but for a separate insert-size library)
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
130 shortPaired2 (see above)
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
131 long (for Sanger, 454 or even reference sequences)
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
132 longPaired
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
133
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
134 </help>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
135 <expand macro="citation"/>
c170448acc8a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/velvet commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
136 </tool>