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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta commit 40b5e586ec4445e121779ce0e0ededf74ed356f7
author artbio
date Sun, 15 Oct 2023 13:34:58 +0000
parents f3c9cbd84728
children
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d25dc80a6a61 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/get_reference_fasta commit 40b5e586ec4445e121779ce0e0ededf74ed356f7
artbio
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1 <tool id="get_fasta_reference" name="get fasta reference" version="0.3.2">
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816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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2 <description>Obtain reference genome sequence</description>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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3 <stdio>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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4 <exit_code range="1:" />
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5 </stdio>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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6 <command><![CDATA[
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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7 cat "$pre_installed_fasta.fields.path" > "$output"
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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8 ]]></command>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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9 <inputs>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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10 <param help="if you wish to have your fasta sequence listed contact instance administrator" label="Select a fasta sequence" name="pre_installed_fasta" type="select">
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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11 <options from_data_table="all_fasta"/>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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12 </param>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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13 </inputs>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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14 <outputs>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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15 <data name="output" label="${pre_installed_fasta.value_label}" format="fasta" />
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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16 </outputs>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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17 <tests>
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18 <test>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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19 <param name="pre_installed_fasta" value="EcR_USP_224.fa"/>
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20 <output name="output" file="EcR_USP_224.fa"/>
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21 </test>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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22 </tests>
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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23 <help><![CDATA[
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24 Places the galaxy instance pre-built genome index sequence in the current history.
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25 Useful for sharing purposes or tools that work directly on fasta files.
816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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26 ]]></help>
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27 <citations>
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28 <citation type="doi">10.1186/gb-2010-11-8-r86</citation>
98211bfc53fc "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit 98d53eb3a7a5f53f3779dbd8e0508c8c3dd338cf"
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29 </citations>
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816bedbb305c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit ff0b4efcce46f70bb06dcb1b7200c348959d1911"
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30 </tool>