Mercurial > repos > drosofff > blast_to_scaffold
comparison blast_to_scaffold.xml @ 4:3288cc5a57e5 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit fb47b9859a0703f1fa4a1e76b75b9dae29ca8329
| author | drosofff |
|---|---|
| date | Fri, 25 Mar 2016 19:21:26 -0400 |
| parents | e279e53a3fde |
| children | 81ffa74cf96e |
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| 3:e279e53a3fde | 4:3288cc5a57e5 |
|---|---|
| 1 <tool id="blast2scaffold" name="blast_to_scaffold" version="0.1.0"> | 1 <tool id="blast2scaffold" name="blast_to_scaffold" version="0.9.0"> |
| 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 </requirements> | 4 </requirements> |
| 5 <command interpreter="python"> | 5 <command interpreter="python"> |
| 6 blast_to_scaffold.py --sequences "$sequences" | 6 blast_to_scaffold.py --sequences "$sequences" |
| 7 --guideSequence "$guideSequence" | 7 --guideSequence "$guideSequence" |
| 8 --blast-tab "$blast_tab" | 8 --blast-tab "$blast_tab" |
| 9 --output "$output" | 9 --output "$output" |
| 10 --scaffold_prefix "$sequences.element_identifier" | |
| 11 --scaffold_suffix "$guideSequence.element_identifier" | |
| 10 </command> | 12 </command> |
| 11 <inputs> | 13 <inputs> |
| 12 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> | 14 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> |
| 13 <param name="guideSequence" type="data" format="fasta" label="Select the fasta guide sequence for scaffolding"/> | 15 <param name="guideSequence" type="data" format="fasta" label="Select the fasta guide sequence for scaffolding"/> |
| 14 <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"/> | 16 <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"/> |