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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold commit 7777a0e34cc2ccd228183af74809ae0d5d9e9b85
author artbio
date Wed, 11 Oct 2023 13:03:33 +0000
parents ec3b8341f551
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1 <tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.1.0"> 1 <tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.1.1">
2 <description>Generate DNA scaffold from blastx alignment of Contigs</description> 2 <description>Generate DNA scaffold from blastx alignment of Contigs</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.7.6">python</requirement> 4 <requirement type="package" version="3.7.6">python</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> 6 <command detect_errors="exit_code"><![CDATA[
7 blastx_to_scaffold.py --sequences $sequences 7 python $__tool_directory__/blastx_to_scaffold.py
8 --sequences $sequences
8 --blastx-tab $blastx_tab 9 --blastx-tab $blastx_tab
9 --output $output 10 --output $output
10 </command> 11 ]]></command>
11 <inputs> 12 <inputs>
12 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> 13 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/>
13 <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"/> 14 <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"/>
14 15
15 </inputs> 16 </inputs>
30 <help> 31 <help>
31 32
32 33
33 **What it Does** 34 **What it Does**
34 This tool starts from DNA contigs that aligned to a subject protein sequence through blastx. 35 This tool starts from DNA contigs that aligned to a subject protein sequence through blastx.
35 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. 36 The contigs must be provided in fasta format. The blastx output must be tabular, the 12 standard
37 columns plus column 13 with the length of the blastx subject.
38
36 The final scaffold is a DNA sequence. 39 The final scaffold is a DNA sequence.
40
37 Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold. 41 Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold.
38 42
39 **Attribution**
40 This Galaxy tool was created by drosofff@gmail.com on 28/05/2015
41 </help> 43 </help>
42 44
45 <citations>
46 <citation type="doi">10.1186/s13742-015-0080-7</citation>
47 </citations>
48
43 </tool> 49 </tool>