Mercurial > repos > artbio > blast_to_scaffold
annotate blast_to_scaffold.xml @ 2:3041f611636f draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
author | artbio |
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date | Wed, 11 Oct 2023 10:34:08 +0000 |
parents | be61d0d0d622 |
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be61d0d0d622
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 3dcf4e7314dd6a4fefcd721ac58c8130dd1da2a1"
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1 <tool id="blast2scaffold" name="blast_to_scaffold" version="1.1.0"> |
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7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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2 <description>Generate DNA scaffold from blastn or tblastx alignment of Contigs</description> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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3 <requirements> |
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be61d0d0d622
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 3dcf4e7314dd6a4fefcd721ac58c8130dd1da2a1"
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4 <requirement type="package" version="3.7.6">python</requirement> |
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7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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5 </requirements> |
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3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
artbio
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6 <command detect_errors="exit_code"><![CDATA[ |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
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7 python $__tool_directory__/blast_to_scaffold.py |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
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8 --sequences "$sequences" |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
artbio
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9 --guideSequence "$guideSequence" |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
artbio
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10 --blast-tab "$blast_tab" |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
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11 --output "$output" |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
artbio
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12 --scaffold_prefix "$sequences.element_identifier" |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
artbio
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13 --scaffold_suffix "$guideSequence.element_identifier" |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
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14 ]]></command> |
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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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15 <inputs> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
artbio
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16 <param name="sequences" type="data" format="fasta" label="Select a fasta contigs file"/> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
artbio
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17 <param name="guideSequence" type="data" format="fasta" label="Select the fasta guide sequence for scaffolding"/> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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18 <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"/> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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19 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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20 </inputs> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
artbio
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21 <outputs> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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22 <data format="fasta" name="output"/> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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23 </outputs> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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24 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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25 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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26 <tests> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
artbio
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27 <test> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
artbio
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28 <param name="sequences" value="contigs.fa" ftype="fasta"/> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
artbio
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29 <param name="blast_tab" value="blast.tab" ftype="tabular"/> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
artbio
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30 <param name="guideSequence" value="guideSequence.fa" ftype="tabular"/> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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31 <output name="output" file="assembly.fa" ftype="fasta"/> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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32 </test> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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33 </tests> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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34 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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35 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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36 <help> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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37 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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38 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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39 **What it Does** |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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40 This tool starts from DNA contigs that aligned to a subject DNA sequence through blastn or tblastx. |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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41 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. |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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42 The sequence used to BLAST (blastn or tblastx) the contigs must be provided to serve as a guide to the final assembly |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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43 The final assembly is a DNA sequence. |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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44 Nucleotides of the guide sequence which were not covered by contigs are in small letters in the output assembly. |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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45 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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46 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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47 **Attribution** |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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48 This Galaxy tool was created by drosofff@gmail.com on 5/01/2016 |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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49 </help> |
7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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50 |
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3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
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51 <citations> |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
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52 <citation type="doi">10.1186/s13742-015-0080-7</citation> |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
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53 </citations> |
3041f611636f
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/blast_to_scaffold commit 22c413141878d86ec10e80ef43ba0da792232cb0
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54 |
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7d96b28eec49
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 48a4098045106f363e92357949b32617a2e868c1
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55 </tool> |