Mercurial > repos > drosofff > blastn_to_scaffold

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