Mercurial > repos > mvdbeek > get_reference_fasta

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
author mvdbeek
date Thu, 25 Feb 2016 07:19:45 -0500
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b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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1 <tool id="get_fasta_reference" name="get fasta reference" version="0.1.1">
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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2 <description>Obtain reference genome sequence</description>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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3 <stdio>
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mvdbeek
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4 <exit_code range="1:" />
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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5 </stdio>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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6 <command><![CDATA[
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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7 cat "$pre_installed_fasta.fields.path" > "$output"
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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8 ]]></command>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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9 <inputs>
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mvdbeek
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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">
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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11 <options from_data_table="all_fasta"/>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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12 </param>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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13 </inputs>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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14 <outputs>
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mvdbeek
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15 <data name="output" label="${pre_installed_fasta.value_label}" format="fasta" />
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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16 </outputs>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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17 <tests>
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mvdbeek
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18 <test>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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19 <param name="pre_installed_fasta" value="EcR_USP_224.fa"/>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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20 <output name="output" file="EcR_USP_224.fa"/>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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21 </test>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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22 </tests>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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23 <help><![CDATA[
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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24
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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25 Places the reference genome sequence in the current history.
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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26 Useful for sharing purposes or tools that work directly on fasta files.
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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27
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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28 ]]></help>
b5c0b28cdfb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/get_reference_fasta commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty
mvdbeek
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29 </tool>