Mercurial > repos > devteam > velvet

annotate velvetg.xml @ 0:08256557922f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
author devteam
date Tue, 13 Oct 2015 16:38:28 -0400
parents
children 5da9a0e2fb2d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
1 <tool id="velvetg" name="velvetg" version="@WRAPPER_VERSION@.0">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
2 <description>Velvet sequence assembler for very short reads</description>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
3 <version_command>velvetg 2&gt;&amp;1 | grep "Version" | sed -e 's/Version //'</version_command>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
4 <macros>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
5 <import>macros.xml</import>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
6 </macros>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
7 <expand macro="requirements"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
8 <expand macro="stdio"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
9 <command interpreter="python">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
10 velvetg_wrapper.py
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
11 '$input.extra_files_path'
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
12 #if $generate_amos.afg == "yes":
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
13 -amos_file $generate_amos.afg
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
14 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
15 #if $unused_reads.generate_unused == "yes":
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
16 -unused_reads $unused_reads.generate_unused
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
17 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
18 $read_trkg
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
19 #if $coverage.cutoff == "auto":
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
20 -cov_cutoff auto
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
21 #elif $coverage.cutoff == "value":
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
22 -cov_cutoff $coverage.cov_cutoff
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
23 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
24 #if $expected.coverage == "auto":
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
25 -exp_cov auto
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
26 #elif $expected.coverage == "value":
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
27 -exp_cov $expected.exp_cov
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
28 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
29 #if $contig_lgth.use_contig_lgth == "yes":
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
30 -min_contig_lgth $contig_lgth.min_contig_lgth
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
31 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
32 #if $reads.paired == "yes":
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
33 #if int($reads.ins_length) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
34 -ins_length $reads.ins_length
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
35 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
36 #if $reads.options.advanced == "yes":
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
37 #if int($reads.options.ins_length_sd) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
38 -ins_length_sd $reads.options.ins_length_sd
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
39 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
40 #if int($reads.options.ins_length2) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
41 -ins_length2 $reads.options.ins_length2
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
42 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
43 #if int($reads.options.ins_length2_sd) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
44 -ins_length2_sd $reads.options.ins_length2_sd
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
45 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
46 #if int($reads.options.ins_length_long) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
47 -ins_length_long $reads.options.ins_length_long
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
48 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
49 #if int($reads.options.ins_length_long_sd) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
50 -ins_length_long_sd $reads.options.ins_length_long_sd
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
51 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
52 #if int($reads.options.max_branch_length) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
53 -max_branch_length $reads.options.max_branch_length
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
54 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
55 #if int($reads.options.max_divergence) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
56 -max_divergence $reads.options.max_divergence
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
57 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
58 #if int($reads.options.max_gap_count) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
59 -max_gap_count $reads.options.max_gap_count
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
60 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
61 #if int($reads.options.min_pair_count) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
62 -min_pair_count $reads.options.min_pair_count
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
63 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
64 #if int($reads.options.max_coverage) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
65 -max_coverage $reads.options.max_coverage
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
66 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
67 #if int($reads.options.long_mult_cutoff) > 0:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
68 -long_mult_cutoff $reads.options.long_mult_cutoff
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
69 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
70 $reads.options.scaffolding
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
71 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
72 #end if
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
73 </command>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
74 <inputs>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
75 <param name="input" type="data" format="velvet" label="Velvet Dataset" help="Prepared by velveth."/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
76 <conditional name="generate_amos">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
77 <param name="afg" type="select" label="Generate a AMOS.afg file">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
78 <option value="no">No</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
79 <option value="yes">Yes</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
80 </param>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
81 <when value="no"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
82 <when value="yes"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
83 </conditional>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
84
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
85 <conditional name="unused_reads">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
86 <param name="generate_unused" type="select" label="Generate a UnusedReads fasta file">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
87 <option value="no">No</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
88 <option value="yes">Yes</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
89 </param>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
90 <when value="no"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
91 <when value="yes"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
92 </conditional>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
93
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
94 <conditional name="last_graph">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
95 <param name="generate_graph" type="select" label="Generate velvet LastGraph file">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
96 <option value="no">No</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
97 <option value="yes">Yes</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
98 </param>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
99 <when value="no"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
100 <when value="yes"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
101 </conditional>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
102
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
103 <param name="read_trkg" type="boolean" checked="false" truevalue="-read_trkg yes" falsevalue="-read_trkg no" label="Tracking of short read positions in assembly" help="Generates Graph2 dataset" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
104
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
105 <conditional name="coverage">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
106 <param name="cutoff" type="select" label="Coverage cutoff" help="">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
107 <option value="none">None</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
108 <option value="auto">Automatically Determined</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
109 <option value="value">Specify Cutoff Value</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
110 </param>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
111 <when value="none"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
112 <when value="auto"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
113 <when value="value">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
114 <param name="cov_cutoff" value="10.0" label="Remove nodes with coverage below" type="float" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
115 </when>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
116 </conditional>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
117
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
118 <conditional name="expected">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
119 <param name="coverage" type="select" label="Expected Coverage of Unique Regions" help="">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
120 <option value="none">None</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
121 <option value="auto">Automatically Determined</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
122 <option value="value">Specify Expected Value</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
123 </param>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
124 <when value="none"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
125 <when value="auto"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
126 <when value="value">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
127 <param name="exp_cov" value="10.0" label="Remove nodes with coverage below" type="float" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
128 </when>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
129 </conditional>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
130
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
131 <conditional name="contig_lgth">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
132 <param name="use_contig_lgth" type="select" label=" Set minimum contig length" help="minimum contig length exported to contigs.fa file (default: hash length * 2).">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
133 <option value="no">No</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
134 <option value="yes">Yes</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
135 </param>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
136 <when value="no"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
137 <when value="yes">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
138 <param name="min_contig_lgth" value="42" label="minimum contig length" type="integer" help="minimum contig length exported to contigs.fa file (default: hash length * 2)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
139 </when>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
140 </conditional>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
141
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
142 <conditional name="reads">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
143 <param name="paired" type="select" label="Using Paired Reads">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
144 <option value="no">No</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
145 <option value="yes" selected="${input.metadata.paired_end_reads}">Yes</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
146 </param>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
147 <when value="no"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
148 <when value="yes">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
149 <param name="ins_length" value="-1" label="Insert Length in Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
150 <conditional name="options">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
151 <param name="advanced" type="select" label="Velvet Advanced Options">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
152 <option value="no">Use Defaults</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
153 <option value="yes">Set Advanced Option Values</option>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
154 </param>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
155 <when value="no"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
156 <when value="yes">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
157 <param name="ins_length_sd" value="-1" label="Estimate of Standard Deviation of Paired-End Read dataset(ignored when -1)" type="integer" help="Estimate of standard deviation of Paired-End Read dataset (default: 10% of corresponding length)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
158 <param name="ins_length2" value="-1" label="Insert Length in 2nd Paired-End Short Read dataset (ignored when -1)" type="integer" help="Expected distance between two paired end reads in the second short-read dataset"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
159 <param name="ins_length2_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of 2nd Paired-End Read dataset (default: 10% of corresponding length)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
160 <param name="ins_length_long" value="-1" label="Insert Length in Long Paired-End Read dataset (ignored when -1)" type="integer" help="Expected distance between two long paired-end reads"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
161 <param name="ins_length_long_sd" value="-1" label="Estimate of Standard Deviation of 2nd Paired-End Read dataset (ignored when -1)" type="integer" help="Estimate of standard deviation of Long Paired-End Read dataset (default: 10% of corresponding length)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
162 <param name="max_branch_length" value="-1" label="Maximum branch length (ignored when -1)" type="integer" help="maximum length in base pair of bubble (default: 100)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
163 <param name="max_divergence" value="-1." label="Maximum max_divergence (between .0 and 1., ignored when -1.)" type="float" help="maximum divergence rate between two branches in a bubble (default: .2)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
164 <param name="max_gap_count" value="-1" label="Maximum gap count (ignored when -1)" type="integer" help="maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
165 <param name="min_pair_count" value="-1" label="Minimum read-pair count (ignored when -1)" type="integer" help="minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
166 <param name="max_coverage" value="-1." label="Maximum coverage exclusion(ignored when -1.)" type="float" help="Exclude data that has coverage more than this maximum coverage value"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
167 <param name="long_mult_cutoff" value="-1" label="Minimum number of long reads required to merge contigs (ignored when -1)" type="integer" help="minimum number of long reads required to merge contigs (default: 2)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
168 <param name="scaffolding" type="boolean" checked="true" truevalue="-scaffolding yes" falsevalue="-scaffolding no" label="Use Scaffolding" help="Scaffold contigs that it cannot quite be connected (This results in sequences of Ns in the contigs)"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
169
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
170 </when>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
171 </conditional>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
172 </when>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
173 </conditional>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
174 </inputs>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
175 <outputs>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
176 <data format="txt" name="Graph2" label="${tool.name} on ${on_string}: Graph2" from_work_dir="Graph2">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
177 <filter>read_trkg is True</filter>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
178 </data>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
179 <data format="txt" name="LastGraph" label="${tool.name} on ${on_string}: LastGraph" from_work_dir="LastGraph">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
180 <filter>last_graph['generate_graph'] == "yes"</filter>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
181 </data>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
182 <data format="afg" name="velvet_asm" label="${tool.name} on ${on_string}: AMOS.afg" from_work_dir="velvet_asm.afg">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
183 <filter>generate_amos['afg'] == "yes"</filter>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
184 </data>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
185 <data format="fasta" name="unused_reads_fasta" label="${tool.name} on ${on_string}: Unused Reads" from_work_dir="UnusedReads.fa">
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
186 <filter>unused_reads['generate_unused'] == "yes"</filter>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
187 </data>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
188 <data format="tabular" name="stats" label="${tool.name} on ${on_string}: Stats" from_work_dir="stats.txt" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
189 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="contigs.fa" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
190 </outputs>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
191 <requirements>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
192 <requirement type="package">velvet</requirement>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
193 </requirements>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
194 <tests>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
195 <test>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
196 <param name="input" value="velveth_test1/output.html" ftype="velvet" >
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
197 <composite_data value='velveth_test1/Sequences' ftype="Sequences"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
198 <composite_data value='velveth_test1/Roadmaps' ftype="Roadmaps"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
199 <composite_data value='velveth_test1/Log'/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
200 </param>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
201 <param name="afg" value="yes" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
202 <param name="generate_unused" value="yes" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
203 <param name="generate_graph" value="no" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
204 <param name="read_trkg" value="-read_trkg no" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
205 <param name="cutoff" value="auto" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
206 <param name="coverage" value="auto" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
207 <param name="use_contig_lgth" value="no" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
208 <param name="paired" value="no" />
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
209 <!--
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
210 <output name="LastGraph" file="velvetg_test1/lastgraph.txt" compare="diff"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
211 -->
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
212 <output name="velvet_asm" file="velvetg_test1/amos.afg" compare="diff"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
213 <output name="unused_reads_fasta" file="velvetg_test1/unusedreads.fa" compare="diff"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
214 <output name="stats" file="velvetg_test1/stats.csv" compare="diff"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
215 <output name="contigs" file="velvetg_test1/contigs.fa" compare="diff"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
216 </test>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
217 </tests>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
218 <help>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
219 **What it does**
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
220
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
221 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.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
222
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
223 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.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
224
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
225 Read the Velvet `documentation`__ for details on using the Velvet Assembler.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
226
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
227 .. _Velvet: http://www.ebi.ac.uk/~zerbino/velvet/
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
228
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
229 .. __: http://www.ebi.ac.uk/~zerbino/velvet/Manual.pdf
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
230
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
231 ------
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
232
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
233 **Input formats**
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
234
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
235 Velvet can input sequence files in the following formats: fasta fastq fasta.gz fastq.gz eland gerald
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
236
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
237 The input files are prepared for the velvet assembler using **velveth**.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
238
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
239 ------
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
240
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
241 **Outputs**
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
242
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
243 **Contigs**
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
244
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
245 The *contigs.fa* file.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
246 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 length threshold, then the contigs shorter than that value are omitted.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
247 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.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
248 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.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
249
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
250 **Stats**
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
251
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
252 The *stats.txt* file.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
253 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.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
254 The in and out columns correspond to the number of arcs on the 5' and 3' ends of the contig respectively.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
255 The coverages in columns short1 cov, short1 Ocov, short2 cov, and short2 Ocov are provided in k-mer coverage (5.1).
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
256 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.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
257
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
258 **LastGraph**
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
259
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
260 The *LastGraph* file.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
261 This file describes in its entirety the graph produced by Velvet.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
262
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
263 **AMOS.afg**
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
264
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
265 The *velvet_asm.afg* file.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
266 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.
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
267 The file describes all the contigs contained in the contigs.fa file (cf 4.2.1).
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
268
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
269 ------
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
270
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
271 **Velvet parameter list**
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
272
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
273 This is a list of implemented Velvetg options::
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
274
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
275 Standard options:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
276 -cov_cutoff floating-point|auto : removal of low coverage nodes AFTER tour bus or allow the system to infer it
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
277 (default: no removal)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
278 -ins_length integer : expected distance between two paired end reads (default: no read pairing)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
279 -read_trkg yes|no : tracking of short read positions in assembly (default: no tracking)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
280 -min_contig_lgth integer : minimum contig length exported to contigs.fa file (default: hash length * 2)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
281 -amos_file yes|no : export assembly to AMOS file (default: no export)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
282 -exp_cov floating point|auto : expected coverage of unique regions or allow the system to infer it
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
283 (default: no long or paired-end read resolution)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
284
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
285 Advanced options:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
286 -ins_length2 integer : expected distance between two paired-end reads in the second short-read dataset (default: no read pairing)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
287 -ins_length_long integer : expected distance between two long paired-end reads (default: no read pairing)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
288 -ins_length*_sd integer : est. standard deviation of respective dataset (default: 10% of corresponding length)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
289 [replace '*' by nothing, '2' or '_long' as necessary]
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
290 -scaffolding yes|no : scaffolding of contigs used paired end information (default: on)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
291 -max_branch_length integer : maximum length in base pair of bubble (default: 100)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
292 -max_divergence floating-point : maximum divergence rate between two branches in a bubble (default: 0.2)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
293 -max_gap_count integer : maximum number of gaps allowed in the alignment of the two branches of a bubble (default: 3)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
294 -min_pair_count integer : minimum number of paired end connections to justify the scaffolding of two long contigs (default: 10)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
295 -max_coverage floating point : removal of high coverage nodes AFTER tour bus (default: no removal)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
296 -long_mult_cutoff int : minimum number of long reads required to merge contigs (default: 2)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
297 -unused_reads yes|no : export unused reads in UnusedReads.fa file (default: no)
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
298
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
299 Output:
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
300 directory/contigs.fa : fasta file of contigs longer than twice hash length
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
301 directory/stats.txt : stats file (tab-spaced) useful for determining appropriate coverage cutoff
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
302 directory/LastGraph : special formatted file with all the information on the final graph
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
303 directory/velvet_asm.afg : (if requested) AMOS compatible assembly file
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
304
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
305 </help>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
306 <expand macro="citation"/>
08256557922f planemo upload commit 4720b3dfa114d790b597fef6ccf3c17e8c11e111
devteam
parents:
diff changeset
307 </tool>