Mercurial > repos > artbio > blastx_to_scaffold

annotate blastx_to_scaffold.xml @ 0:bdf781f2658b 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/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
author artbio
date Sun, 15 Oct 2017 13:16:03 -0400
parents
children ec3b8341f551
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
1 <tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.0.0">
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
2 <description>Generate DNA scaffold from blastx alignment of Contigs</description>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
3 <requirements>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
4 </requirements>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
5 <command interpreter="python">
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
6 blastx_to_scaffold.py --sequences $sequences
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
7 --blastx-tab $blastx_tab
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
8 --output $output
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
9 </command>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
10 <inputs>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
11 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
12 <param name="blastx_tab" type="data" format="tabular" label="Select a blastx output from your history" help="must have 13 columns with column 13 containing the subject lenght, other columns are standard"/>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
13
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
14 </inputs>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
15 <outputs>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
16 <data format="fasta" name="output"/>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
17 </outputs>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
18
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
19
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
20 <tests>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
21 <test>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
22 <param name="sequences" value="contigs.fa" ftype="fasta"/>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
23 <param name="blastx_tab" value="blastx.tab" ftype="tabular"/>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
24 <output name="output" file="scaffold.fa" ftype="fasta"/>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
25 </test>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
26 </tests>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
27
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
28
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
29 <help>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
30
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
31
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
32 **What it Does**
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
33 This tool starts from DNA contigs that aligned to a subject protein sequence through blastx.
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
34 The contigs must be provided in fasta format. The blastx output must be tabular, the 12 standard column plus column 13 with the length of the blastx subject.
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
35 The final scaffold is a DNA sequence.
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
36 Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold.
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
37
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
38 **Attribution**
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
39 This Galaxy tool was created by drosofff@gmail.com on 28/05/2015
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
40 </help>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
41
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
artbio
parents:
diff changeset
42 </tool>