Mercurial > repos > artbio > blast_to_scaffold
comparison blast_to_scaffold.xml @ 2:3041f611636f draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
| author | artbio |
|---|---|
| date | Wed, 11 Oct 2023 10:34:08 +0000 |
| parents | be61d0d0d622 |
| children |
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| 1:be61d0d0d622 | 2:3041f611636f |
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| 1 <tool id="blast2scaffold" name="blast_to_scaffold" version="1.1.0"> | 1 <tool id="blast2scaffold" name="blast_to_scaffold" version="1.1.0"> |
| 2 <description>Generate DNA scaffold from blastn or tblastx alignment of Contigs</description> | 2 <description>Generate DNA scaffold from blastn or tblastx 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 blast_to_scaffold.py --sequences "$sequences" | 7 python $__tool_directory__/blast_to_scaffold.py |
| 8 --guideSequence "$guideSequence" | 8 --sequences "$sequences" |
| 9 --blast-tab "$blast_tab" | 9 --guideSequence "$guideSequence" |
| 10 --output "$output" | 10 --blast-tab "$blast_tab" |
| 11 --scaffold_prefix "$sequences.element_identifier" | 11 --output "$output" |
| 12 --scaffold_suffix "$guideSequence.element_identifier" | 12 --scaffold_prefix "$sequences.element_identifier" |
| 13 </command> | 13 --scaffold_suffix "$guideSequence.element_identifier" |
| 14 ]]></command> | |
| 14 <inputs> | 15 <inputs> |
| 15 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> | 16 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> |
| 16 <param name="guideSequence" type="data" format="fasta" label="Select the fasta guide sequence for scaffolding"/> | 17 <param name="guideSequence" type="data" format="fasta" label="Select the fasta guide sequence for scaffolding"/> |
| 17 <param name="blast_tab" type="data" format="tabular" label="Select a blastn or tblastx output from your history" help="must have 13 columns with column 13 containing the subject lenght, other columns are standard"/> | 18 <param name="blast_tab" type="data" format="tabular" label="Select a blastn or tblastx output from your history" help="must have 13 columns with column 13 containing the subject lenght, other columns are standard"/> |
| 18 | 19 |
| 45 | 46 |
| 46 **Attribution** | 47 **Attribution** |
| 47 This Galaxy tool was created by drosofff@gmail.com on 5/01/2016 | 48 This Galaxy tool was created by drosofff@gmail.com on 5/01/2016 |
| 48 </help> | 49 </help> |
| 49 | 50 |
| 51 <citations> | |
| 52 <citation type="doi">10.1186/s13742-015-0080-7</citation> | |
| 53 </citations> | |
| 54 | |
| 50 </tool> | 55 </tool> |