Mercurial > repos > bvalot > fasta_filter_0_1

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planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
author bvalot
date Tue, 14 Jun 2022 08:15:55 +0000
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bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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1 <tool id="fasta_filter_region_wrapper" name="Filter region" version="0.1">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.78">biopython</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" />
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8 </stdio>
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9 <version_command>$__tool_directory__/fasta_filter_to_region.py -v</version_command>
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10 <command>
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11 $__tool_directory__/fasta_filter_to_region.py
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12 -o '$output'
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13 '$fasta'
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14 #for $reg in $regions.split(" ")
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15 '$reg'
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16 #end for
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17 </command>
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18 <inputs>
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19 <param name="fasta" type="data" format="fasta" label="Database to filter on fasta" help="FASTA format" />
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20 <param name="regions" type="text" value="" optional="false" size="4X50"
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21 label="List of region to conserved in format accession:start-stop"
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22 help="Separated each regions by a space" />
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="fasta" label="${tool.name} on ${on_string}: fasta" />
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26 </outputs>
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27 <tests>
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28 <test expect_num_outputs="1">
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29 <param name="fasta" value="input.fasta" />
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30 <param name="regions" value="NODE_1_length_344587_cov_27.773165:10-190" />
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31 <output name="output" file="filter_region.fasta" ftype="fasta" />
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32 </test>
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33 </tests>
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34 <help>
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35 **What it does**
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bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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37 Filter a fasta file based on regions.
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39 **Examples**
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41 CP000822.1:458-1689
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bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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43 NODE_1_length_721117_cov_11.496472:14500-18320
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44
bc23da9d464c planemo upload for repository http://172.20.124.12:3000/bvalot3/PythonScript commit 9676573ee48ce5343600ab45cd3ac1a6adddabe4
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45 **Citation et licences**
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46
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47 This Galaxy tool is Copyright © 2018 `B. Valot` and is released
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48 under the `GPL3 license`.
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49
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50 </help>
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51 <citations>
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52 </citations>
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53 </tool>