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annotate blastx_to_scaffold.xml @ 1:ec3b8341f551 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 3dcf4e7314dd6a4fefcd721ac58c8130dd1da2a1"
author artbio
date Wed, 10 Mar 2021 19:11:14 +0000
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children f03154ac4ed8
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ec3b8341f551 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 3dcf4e7314dd6a4fefcd721ac58c8130dd1da2a1"
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1 <tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.1.0">
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bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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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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ec3b8341f551 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 3dcf4e7314dd6a4fefcd721ac58c8130dd1da2a1"
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4 <requirement type="package" version="3.7.6">python</requirement>
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bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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5 </requirements>
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6 <command interpreter="python">
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7 blastx_to_scaffold.py --sequences $sequences
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8 --blastx-tab $blastx_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"/>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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13 <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"/>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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15 </inputs>
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16 <outputs>
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17 <data format="fasta" name="output"/>
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18 </outputs>
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bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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21 <tests>
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22 <test>
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23 <param name="sequences" value="contigs.fa" ftype="fasta"/>
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24 <param name="blastx_tab" value="blastx.tab" ftype="tabular"/>
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25 <output name="output" file="scaffold.fa" ftype="fasta"/>
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26 </test>
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27 </tests>
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bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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30 <help>
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bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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33 **What it Does**
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34 This tool starts from DNA contigs that aligned to a subject protein sequence through blastx.
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35 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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36 The final scaffold is a DNA sequence.
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37 Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold.
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39 **Attribution**
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40 This Galaxy tool was created by drosofff@gmail.com on 28/05/2015
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41 </help>
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43 </tool>