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annotate blast_to_scaffold.xml @ 2:4be47f92e0f7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 030207144f0811822dbdda9a10e036ff8e794d7c
author drosofff
date Fri, 25 Mar 2016 19:13:31 -0400
parents 991bf4769500
children f7474298b40a
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4be47f92e0f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 030207144f0811822dbdda9a10e036ff8e794d7c
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1 <tool id="blast2scaffold" name="blast_to_scaffold" version="0.1.0">
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2 <description>Generate DNA scaffold from blastn or tblastx alignment of Contigs</description>
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3 <requirements>
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4 </requirements>
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5 <command interpreter="python">
a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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6 blast_to_scaffold.py --sequences "$sequences"
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4be47f92e0f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 030207144f0811822dbdda9a10e036ff8e794d7c
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7 --guideSequence "$guideSequence"
4be47f92e0f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 030207144f0811822dbdda9a10e036ff8e794d7c
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8 --blast-tab "$blast_tab"
4be47f92e0f7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 030207144f0811822dbdda9a10e036ff8e794d7c
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9 --output "$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"/>
a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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13 <param name="guideSequence" type="data" format="fasta" label="Select the fasta guide sequence for scaffolding"/>
a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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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"/>
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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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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="blast_tab" value="blast.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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32 <help>
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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 or tblastx.
a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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37 The contigs must be provided in fasta format. The blastn or tblastx output must be tabular, the 12 standard column plus column 13 with the length of the blastn or tblastx subject.
a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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38 The sequence used to BLAST (blastn or tblastx) 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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43 **Attribution**
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44 This Galaxy tool was created by drosofff@gmail.com on 5/01/2016
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45 </help>
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47 </tool>