Mercurial > repos > drosofff > blastx_to_scaffold

annotate blastx_to_scaffold.xml @ 0:6af7f779eb55 draft

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author drosofff
date Tue, 09 Jun 2015 05:37:23 -0400
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1 <tool id="blastx2scaffold" name="blastx_to_scaffold" version="0.9.0">
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2 <description>Generate DNA scaffold from blastx 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 blastx_to_scaffold.py --sequences $sequences
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7 --blastx-tab $blastx_tab
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8 --output $output
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9 </command>
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10 <inputs>
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11 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/>
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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"/>
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13
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14 </inputs>
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15 <outputs>
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16 <data format="fasta" name="output"/>
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17 </outputs>
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18
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19
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20 <tests>
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21 <test>
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22 <param name="sequences" value="contigs.fa" ftype="fasta"/>
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23 <param name="blastx_tab" value="blastx.tab" ftype="tabular"/>
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24 <output name="output" file="scaffold.fa" ftype="fasta"/>
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25 </test>
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26 </tests>
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27
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28
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29 <help>
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30
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31
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32 **What it Does**
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33 This tool start from DNA contigs that aligned to a subject protein sequence through blastx.
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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.
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35 The final scaffold is a DNA sequence.
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36 Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold.
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37
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38 **Attribution**
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39 This Galaxy tool was created by drosofff@gmail.com on 28/05/2015
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40 </help>
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41
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42 </tool>