Mercurial > repos > drosofff > blastn_to_scaffold
comparison blastn_to_scaffold.xml @ 0:ad9a1c117ac6 draft default tip
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
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| date | Sun, 21 Jun 2015 14:41:10 -0400 |
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| -1:000000000000 | 0:ad9a1c117ac6 |
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| 1 <tool id="blastn2scaffold" name="blastn_to_scaffold" version="0.1.0"> | |
| 2 <description>Generate DNA scaffold from blastn alignment of Contigs</description> | |
| 3 <requirements> | |
| 4 </requirements> | |
| 5 <command interpreter="python"> | |
| 6 blastn_to_scaffold.py --sequences $sequences | |
| 7 --guideSequence $guideSequence | |
| 8 --blastn-tab $blastn_tab | |
| 9 --output $output | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <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"/> | |
| 14 <param name="blastn_tab" type="data" format="tabular" label="Select a blastn output from your history" help="must have 13 columns with column 13 containing the subject lenght, other columns are standard"/> | |
| 15 | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="fasta" name="output"/> | |
| 19 </outputs> | |
| 20 | |
| 21 | |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="sequences" value="contigs.fa" ftype="fasta"/> | |
| 25 <param name="blastn_tab" value="blastn.tab" ftype="tabular"/> | |
| 26 <param name="guideSequence" value="guideSequence.fa" ftype="tabular"/> | |
| 27 <output name="output" file="assembly.fa" ftype="fasta"/> | |
| 28 </test> | |
| 29 </tests> | |
| 30 | |
| 31 | |
| 32 <help> | |
| 33 | |
| 34 | |
| 35 **What it Does** | |
| 36 This tool start from DNA contigs that aligned to a subject DNA sequence through blastn. | |
| 37 The contigs must be provided in fasta format. The blastn output must be tabular, the 12 standard column plus column 13 with the length of the blastn subject. | |
| 38 The sequence used to blastn the contigs must be provided to serve as a guide to the final assembly | |
| 39 The final assembly is a DNA sequence. | |
| 40 Nucleotides of the guide sequence which were not covered by contigs are in small letters in the output assembly. | |
| 41 | |
| 42 | |
| 43 **Attribution** | |
| 44 This Galaxy tool was created by drosofff@gmail.com on 9/06/2015 | |
| 45 </help> | |
| 46 | |
| 47 </tool> |