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comparison create_gffdb.xml @ 1:8880c2e4b2ee draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/gffutils commit eeb6499c828d0a99b6a891ed88de690cc1b8aeed-dirty
author jjohnson
date Mon, 16 Apr 2018 18:14:30 -0400
parents 8ba71aead5bc
children b956465b8893
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0:8ba71aead5bc 1:8880c2e4b2ee
1 <tool id="create_gffdb" name="Create GFF DB for GTF or GFF3" version="0.1.0"> 1 <tool id="create_gffdb" name="Create gffutils SQLite DB" version="0.1.0">
2 <description>gffutils sqlite db</description> 2 <description>for GTF or GFF3</description>
3 <requirements> 3 <requirements>
4 <requirement type="package">gffutils</requirement> 4 <requirement type="package">gffutils</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 python '$__tool_directory__/create_gffdb.py' '$input' '$output' 7 python '$__tool_directory__/create_gffdb.py' $create_introns '$input' '$output'
8 ]]></command> 8 ]]></command>
9 <inputs> 9 <inputs>
10 <param name="input" type="data" format="gtf,gff3" label="GTF or GFF3 Annotation"/> 10 <param name="input" type="data" format="gtf,gff3" label="GTF or GFF3 Annotation"/>
11 <param name="create_introns" type="boolean" truevalue="--create_introns" falsevalue="" checked="false"
12 label="create intron features"/>
13 <param name="disable_infer_transcripts" type="boolean" truevalue="--disable_infer_transcripts" falsevalue="" checked="true"
14 label="disable_infer_transcripts (True for Ensmbl GTF)"
15 help="Can be more than 100 times slower if this is false"/>
16 <param name="disable_infer_genes" type="boolean" truevalue="--disable_infer_genes" falsevalue="" checked="true"
17 label="disable_infer_transcripts (True for Ensmbl GTF)"
18 help="Can be more than 100 times slower if this is false"/>
11 </inputs> 19 </inputs>
12 <outputs> 20 <outputs>
13 <data name="output" format="sqlite" label="${tool.name} ${input.name}.sqlite" /> 21 <data name="output" format="sqlite" label="${tool.name} ${input.name}.sqlite" />
14 </outputs> 22 </outputs>
15 <tests> 23 <tests>
21 <param name="input" ftype="gff3" value="GRCm38.gff3"/> 29 <param name="input" ftype="gff3" value="GRCm38.gff3"/>
22 <output name="output" file="GRCm38.gff3.sqlite" ftype="sqlite" compare="sim_size" delta="5000" /> 30 <output name="output" file="GRCm38.gff3.sqlite" ftype="sqlite" compare="sim_size" delta="5000" />
23 </test> 31 </test>
24 </tests> 32 </tests>
25 <help><![CDATA[ 33 <help><![CDATA[
34 Creates a SQLite database for a GTF or GFF3 feature file.
35 http://daler.github.io/gffutils/index.html
26 ]]></help> 36 ]]></help>
27 </tool> 37 </tool>