Mercurial > repos > drosofff > msp_blastparser_and_hits

annotate BlastParser_and_hits.xml @ 6:3f7cfa1cf90c 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 e511de70e387d5033ab91f37c8ddb5665fa61a87
author drosofff
date Mon, 14 Sep 2015 11:39:51 -0400
parents a941981a298c
children 72ef366ef55e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
3f7cfa1cf90c planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit e511de70e387d5033ab91f37c8ddb5665fa61a87
drosofff
parents: 5
diff changeset
1 <tool id="BlastParser_and_hits" name="Parse blast output and compile hits" version="2.3.0">
0
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
2 <description>for virus discovery</description>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
3 <requirements></requirements>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
4 <command interpreter="python">
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
5 BlastParser_and_hits.py
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
6 --sequences $sequences
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
7 --blast $blast
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
8 --tabularOutput $tabularOutput
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
9 --fastaOutput $fastaOutput
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
10 --flanking $flanking
2
e0985bad7b92 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
11 --mode $mode
4
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
12 ## Additional parameters.
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
13 #if $additional_filters.use_filters == "yes":
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
14 --filter_relativeCov $additional_filters.filter_relativeCov
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
15 --filter_maxScore $additional_filters.filter_maxScore
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
16 --filter_meanScore $additional_filters.filter_meanScore
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
17 #end if
6
3f7cfa1cf90c planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit e511de70e387d5033ab91f37c8ddb5665fa61a87
drosofff
parents: 5
diff changeset
18 --al_sequences $al_sequences
3f7cfa1cf90c planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit e511de70e387d5033ab91f37c8ddb5665fa61a87
drosofff
parents: 5
diff changeset
19 --un_sequences $un_sequences
4
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
20
0
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
21 </command>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
22 <inputs>
3959a271cf3f 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" />
3959a271cf3f 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" />
3959a271cf3f 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"/>
2
e0985bad7b92 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
26 <param name="mode" type="select" label="Verbose or short reporting mode" help="display or not the oases contigs">
e0985bad7b92 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
27 <option value="verbose" default="true">verbose</option>
e0985bad7b92 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
28 <option value="short">do not report oases contigs</option>
e0985bad7b92 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
29 </param>
4
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
30 <conditional name="additional_filters">
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
31 <param name="use_filters" type="select" label="Use Additional Filters?">
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
32 <option value="no">No</option>
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
33 <option value="yes">Yes</option>
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
34 </param>
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
35 <when value="no">
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
36 </when>
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
37 <when value="yes">
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
38 <param name="filter_relativeCov" type="float" value="0" max="1" label="Minimum Relative Subject Coverage" help=""/>
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
39 <param name="filter_maxScore" type="float" value="0" label="Minimum maximum BitScore" help=""/>
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
40 <param name="filter_meanScore" type="float" value="0" label="Minimum mean BitScore" help=""/>
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
41 </when>
22641bb68b91 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 2
diff changeset
42 </conditional>
0
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
43 </inputs>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
44 <outputs>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
45 <data name="tabularOutput" format="tabular" label="blast analysis, by subjects"/>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
46 <data name="fastaOutput" format="fasta" label="hits"/>
6
3f7cfa1cf90c planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit e511de70e387d5033ab91f37c8ddb5665fa61a87
drosofff
parents: 5
diff changeset
47 <data name="al_sequences" format="fasta" label="Blast aligned sequences"/>
3f7cfa1cf90c planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit e511de70e387d5033ab91f37c8ddb5665fa61a87
drosofff
parents: 5
diff changeset
48 <data name="un_sequences" format="fasta" label="Blast unaligned sequences"/>
0
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
49 </outputs>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
50
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
51 <tests>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
52 <test>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
53 <param ftype="fasta" name="sequences" value="input.fa" />
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
54 <param ftype="tabular" name="blast" value="blast.tab" />
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
55 <param name="flanking" value="5" />
5
a941981a298c planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 4
diff changeset
56 <param name="use_filters" value="no" />
2
e0985bad7b92 planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents: 0
diff changeset
57 <param name="mode" value="verbose" />
0
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
58 <output name="tabularOutput" ftype="tabular" file="output.tab" />
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
59 <output name="fastaOutput" ftype="fasta" file="output.fa" />
6
3f7cfa1cf90c planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit e511de70e387d5033ab91f37c8ddb5665fa61a87
drosofff
parents: 5
diff changeset
60 <output name="al_sequences" ftype="fasta" file="al_sequences.fa" />
3f7cfa1cf90c planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit e511de70e387d5033ab91f37c8ddb5665fa61a87
drosofff
parents: 5
diff changeset
61 <output name="un_sequences" ftype="fasta" file="un_sequences.fa" />
0
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
62 </test>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
63 </tests>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
64
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
65 <help>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
66
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
67 **What it does**
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
68
6
3f7cfa1cf90c planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit e511de70e387d5033ab91f37c8ddb5665fa61a87
drosofff
parents: 5
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
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
70
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
71 </help>
3959a271cf3f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
72 </tool>