Mercurial > repos > artbio > blastx_to_scaffold
comparison blastx_to_scaffold.xml @ 0:bdf781f2658b draft
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 |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:bdf781f2658b |
|---|---|
| 1 <tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.0.0"> | |
| 2 <description>Generate DNA scaffold from blastx alignment of Contigs</description> | |
| 3 <requirements> | |
| 4 </requirements> | |
| 5 <command interpreter="python"> | |
| 6 blastx_to_scaffold.py --sequences $sequences | |
| 7 --blastx-tab $blastx_tab | |
| 8 --output $output | |
| 9 </command> | |
| 10 <inputs> | |
| 11 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> | |
| 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"/> | |
| 13 | |
| 14 </inputs> | |
| 15 <outputs> | |
| 16 <data format="fasta" name="output"/> | |
| 17 </outputs> | |
| 18 | |
| 19 | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name="sequences" value="contigs.fa" ftype="fasta"/> | |
| 23 <param name="blastx_tab" value="blastx.tab" ftype="tabular"/> | |
| 24 <output name="output" file="scaffold.fa" ftype="fasta"/> | |
| 25 </test> | |
| 26 </tests> | |
| 27 | |
| 28 | |
| 29 <help> | |
| 30 | |
| 31 | |
| 32 **What it Does** | |
| 33 This tool starts from DNA contigs that aligned to a subject protein sequence through blastx. | |
| 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. | |
| 35 The final scaffold is a DNA sequence. | |
| 36 Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold. | |
| 37 | |
| 38 **Attribution** | |
| 39 This Galaxy tool was created by drosofff@gmail.com on 28/05/2015 | |
| 40 </help> | |
| 41 | |
| 42 </tool> |