Mercurial > repos > drosofff > msp_blastparser_and_hits

annotate BlastParser_and_hits.xml @ 4:60b6bd959929 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
author drosofff
date Fri, 15 Jan 2016 12:29:30 -0500
parents 8f5d48294f70
children 78c34df2dd8d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.3">
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 $additional_filters.filter_meanScore
4
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
17 --filter_term_in "$additional_filters.filter_term_in"
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
18 --filter_term_out "$additional_filters.filter_term_out"
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
19 #end if
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
20 --al_sequences $al_sequences
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
21 --un_sequences $un_sequences
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
22
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
23 </command>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
24 <inputs>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
25 <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
26 <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
27 <param name="flanking" type="text" size="5" value= "5" label="Number of flanking nucleotides to add to hits for CAP3 assembly"/>
3
8f5d48294f70 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3d9ddd0f6f3c3b97a3bebf52646731ad6771e178
drosofff
parents: 2
diff changeset
28 <param name="mode" type="select" label="Extensive or compact reporting mode" help="display (extensive) or not (compact) the oases contigs">
8f5d48294f70 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3d9ddd0f6f3c3b97a3bebf52646731ad6771e178
drosofff
parents: 2
diff changeset
29 <option value="verbose" default="true">extensive</option>
8f5d48294f70 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3d9ddd0f6f3c3b97a3bebf52646731ad6771e178
drosofff
parents: 2
diff changeset
30 <option value="short">compact</option>
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
31 </param>
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
32 <conditional name="additional_filters">
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
33 <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
34 <option value="no">No</option>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
35 <option value="yes">Yes</option>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
36 </param>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
37 <when value="no">
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
38 </when>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
39 <when value="yes">
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
40 <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
41 <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
42 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
4
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
43 <param name="filter_term_in" type="text" value="" label="filter the subject list with a keyword" help=""/>
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
44 <param name="filter_term_out" type="text" value="" label="filter the subject list excluding a keyword" help=""/>
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
45 </when>
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
46 </conditional>
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
47 </inputs>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
48 <outputs>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
49 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
50 <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
51 <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
52 <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
53 </outputs>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
54
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
55 <tests>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
56 <test>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
57 <param ftype="fasta" name="sequences" value="input.fa" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
58 <param ftype="tabular" name="blast" value="blast.tab" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
59 <param name="flanking" value="5" />
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
60 <param name="use_filters" value="no" />
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
61 <param name="mode" value="verbose" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
62 <output name="tabularOutput" ftype="tabular" file="output.tab" />
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
63 <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
64 <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
65 <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
66 </test>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
67 </tests>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
68
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
69 <help>
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 **What it does**
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
72
2
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
73 Parse blast outputs for viruses genome assembly. Outputs analysis and hit sequences for further assembly. Outputs also the contig sequences which have or not been blast aligned taking into account all indicated cut-offs
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
74
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
75 </help>
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
76 </tool>