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annotate create_gffdb.xml @ 0:8ba71aead5bc draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
author jjohnson
date Sun, 08 Apr 2018 13:26:47 -0400
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children 8880c2e4b2ee
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8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
jjohnson
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1 <tool id="create_gffdb" name="Create GFF DB for GTF or GFF3" version="0.1.0">
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
jjohnson
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2 <description>gffutils sqlite db</description>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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3 <requirements>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
jjohnson
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4 <requirement type="package">gffutils</requirement>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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5 </requirements>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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6 <command detect_errors="exit_code"><![CDATA[
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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7 python '$__tool_directory__/create_gffdb.py' '$input' '$output'
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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8 ]]></command>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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9 <inputs>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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10 <param name="input" type="data" format="gtf,gff3" label="GTF or GFF3 Annotation"/>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
jjohnson
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11 </inputs>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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12 <outputs>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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13 <data name="output" format="sqlite" label="${tool.name} ${input.name}.sqlite" />
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
jjohnson
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14 </outputs>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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15 <tests>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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16 <test>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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17 <param name="input" ftype="gtf" value="GRCm38.gtf"/>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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18 <output name="output" file="GRCm38.gtf.sqlite" ftype="sqlite" compare="sim_size" delta="5000" />
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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19 </test>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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20 <test>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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21 <param name="input" ftype="gff3" value="GRCm38.gff3"/>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
jjohnson
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22 <output name="output" file="GRCm38.gff3.sqlite" ftype="sqlite" compare="sim_size" delta="5000" />
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
jjohnson
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23 </test>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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24 </tests>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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25 <help><![CDATA[
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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26 ]]></help>
8ba71aead5bc planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit 186424e18ed21f2aea293fa7c4b654a9a4fb5d8c-dirty
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27 </tool>