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annotate create_gffdb.xml @ 2:b956465b8893 draft default tip

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit f84d4d6e7fa7617e4b8298007db22e1355071213-dirty
author jjohnson
date Tue, 17 Apr 2018 10:19:30 -0400
parents 8880c2e4b2ee
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jjohnson
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1 <tool id="create_gffdb" name="Create gffutils SQLite DB" version="0.1.0">
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2 <description>for GTF or GFF3</description>
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3 <requirements>
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4 <requirement type="package">gffutils</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 python '$__tool_directory__/create_gffdb.py' $disable_infer_transcripts $disable_infer_genes $create_introns '$input' '$output'
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8 ]]></command>
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9 <inputs>
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10 <param name="input" type="data" format="gtf,gff3" label="GTF or GFF3 Annotation"/>
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11 <param name="create_introns" type="boolean" truevalue="--create_introns" falsevalue="" checked="false"
8880c2e4b2ee planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
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12 label="create intron features"/>
8880c2e4b2ee planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
jjohnson
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13 <param name="disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="true"
8880c2e4b2ee planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
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14 label="disable_infer_transcripts (True for Ensmbl GTF)"
8880c2e4b2ee planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
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15 help="Can be more than 100 times slower if this is false"/>
8880c2e4b2ee planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
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16 <param name="disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="true"
8880c2e4b2ee planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
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17 label="disable_infer_transcripts (True for Ensmbl GTF)"
8880c2e4b2ee planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
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18 help="Can be more than 100 times slower if this is false"/>
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19 </inputs>
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20 <outputs>
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21 <data name="output" format="sqlite" label="${tool.name} ${input.name}.sqlite" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input" ftype="gtf" value="GRCm38.gtf"/>
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26 <output name="output" file="GRCm38.gtf.sqlite" ftype="sqlite" compare="sim_size" delta="5000" />
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27 </test>
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28 <test>
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29 <param name="input" ftype="gff3" value="GRCm38.gff3"/>
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30 <output name="output" file="GRCm38.gff3.sqlite" ftype="sqlite" compare="sim_size" delta="5000" />
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 Creates a SQLite database for a GTF or GFF3 feature file.
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35 http://daler.github.io/gffutils/index.html
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36 ]]></help>
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37 </tool>