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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold commit 7777a0e34cc2ccd228183af74809ae0d5d9e9b85
author artbio
date Wed, 11 Oct 2023 13:03:33 +0000
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f03154ac4ed8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold commit 7777a0e34cc2ccd228183af74809ae0d5d9e9b85
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1 <tool id="blastx2scaffold" name="blastx_to_scaffold" version="1.1.1">
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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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5 </requirements>
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f03154ac4ed8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold commit 7777a0e34cc2ccd228183af74809ae0d5d9e9b85
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6 <command detect_errors="exit_code"><![CDATA[
f03154ac4ed8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold commit 7777a0e34cc2ccd228183af74809ae0d5d9e9b85
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7 python $__tool_directory__/blastx_to_scaffold.py
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8 --sequences $sequences
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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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9 --blastx-tab $blastx_tab
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10 --output $output
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11 ]]></command>
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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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12 <inputs>
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13 <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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14 <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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16 </inputs>
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17 <outputs>
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18 <data format="fasta" name="output"/>
bdf781f2658b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blastx_to_scaffold commit 1353e75b8459213e88f32744a759ce4d7b43826d
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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="blastx_tab" value="blastx.tab" ftype="tabular"/>
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26 <output name="output" file="scaffold.fa" ftype="fasta"/>
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27 </test>
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28 </tests>
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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31 <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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34 **What it Does**
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35 This tool starts from DNA contigs that aligned to a subject protein sequence through blastx.
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36 The contigs must be provided in fasta format. The blastx output must be tabular, the 12 standard
f03154ac4ed8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold commit 7777a0e34cc2ccd228183af74809ae0d5d9e9b85
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37 columns plus column 13 with the length of the blastx subject.
f03154ac4ed8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold commit 7777a0e34cc2ccd228183af74809ae0d5d9e9b85
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38
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39 The final scaffold is a DNA sequence.
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f03154ac4ed8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blastx_to_scaffold commit 7777a0e34cc2ccd228183af74809ae0d5d9e9b85
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41 Sequences of the subject protein which were not aligned to the contigs are replaced by Ns in this scaffold.
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43 </help>
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45 <citations>
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46 <citation type="doi">10.1186/s13742-015-0080-7</citation>
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47 </citations>
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48
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49 </tool>