Mercurial > repos > drosofff > msp_blastparser_and_hits

annotate BlastParser_and_hits.xml @ 1:1964514aabde draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
author drosofff
date Mon, 14 Sep 2015 12:18:46 -0400
parents 69ea2a13947f
children bb0d4cd765c5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.0">
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
2 <description>for virus discovery</description>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
3 <requirements></requirements>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
4 <command interpreter="python">
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
5 BlastParser_and_hits.py
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
6 --sequences $sequences
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
7 --blast $blast
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
8 --tabularOutput $tabularOutput
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
9 --fastaOutput $fastaOutput
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
10 --flanking $flanking
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
11 --mode $mode
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
12 ## Additional parameters.
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
13 #if $additional_filters.use_filters == "yes":
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
14 --filter_relativeCov $additional_filters.filter_relativeCov
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
15 --filter_maxScore $additional_filters.filter_maxScore
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
16 --filter_meanScore $additional_filters.filter_meanScore
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
17 #end if
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
18 --al_sequences $al_sequences
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
19 --un_sequences $un_sequences
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
20
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
21 </command>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
22 <inputs>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
23 <param name="sequences" type="data" format="fasta" label="fasta sequences that have been blasted" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
24 <param name="blast" type="data" format="tabular" label="The blast output you wish to parse" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
25 <param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
26 <param name="mode" type="select" label="Verbose or short reporting mode" help="display or not the oases contigs">
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
27 <option value="verbose" default="true">verbose</option>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
28 <option value="short">do not report oases contigs</option>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
29 </param>
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
30 <conditional name="additional_filters">
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
31 <param name="use_filters" type="select" label="Use Additional Filters?">
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
32 <option value="no">No</option>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
33 <option value="yes">Yes</option>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
34 </param>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
35 <when value="no">
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
36 </when>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
37 <when value="yes">
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
38 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
39 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
40 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
41 </when>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
42 </conditional>
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
43 </inputs>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
44 <outputs>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
45 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
46 <data name="fastaOutput" format="fasta" label="hits"/>
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
47 <data name="al_sequences" format="fasta" label="Blast aligned sequences"/>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
48 <data name="un_sequences" format="fasta" label="Blast unaligned sequences"/>
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
49 </outputs>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
50
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
51 <tests>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
52 <test>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
53 <param ftype="fasta" name="sequences" value="input.fa" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
54 <param ftype="tabular" name="blast" value="blast.tab" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
55 <param name="flanking" value="5" />
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
56 <param name="use_filters" value="no" />
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
57 <param name="mode" value="verbose" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
58 <output name="tabularOutput" ftype="tabular" file="output.tab" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
59 <output name="fastaOutput" ftype="fasta" file="output.fa" />
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
60 <output name="al_sequences" ftype="fasta" file="al_sequences.fa" />
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
61 <output name="un_sequences" ftype="fasta" file="un_sequences.fa" />
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
62 </test>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
63 </tests>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
64
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
65 <help>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
66
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
67 **What it does**
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
68
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
69 Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly. Output also the contig sequences which have or not been blast aligned with the indicated cut-off
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
70
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
71 </help>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
72 </tool>