Mercurial > repos > iracooke > protk_proteogenomics

comparison gff3_to_fasta.xml @ 2:68d8c9e521d7 draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:34:50 -0400
parents 28067ed4ea0e
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1:a85c8de9630a 2:68d8c9e521d7
1 <tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.0"> 1 <tool id="gff3_to_fasta" name="Extract proteins from gff3" version="1.1.1">
2 <requirements> 2 <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description>
3 <container type="docker">iracooke/protk-1.4.1</container> 3 <requirements>
4 <requirement type="package" version="1.4">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="1.4.3">protk</requirement>
5 </requirements> 6 </requirements>
6 7 <stdio>
7 <description>Extract proteins from gff3 and encode genomic coordinates in the fasta header</description> 8 <exit_code range="1:" level="fatal" description="Failure" />
8 9 </stdio>
9 <command> 10 <command>
10 augustus_to_proteindb.rb $gff_file -o $output $coords 11 augustus_to_proteindb.rb $gff_file -o $output $coords
11 </command> 12 </command>
12 13 <inputs>
13 14 <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" />
14 15 <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" />
15 16 </inputs>
16 <stdio> 17 <outputs>
17 <exit_code range="1:" level="fatal" description="Failure" /> 18 <data format="fasta" name="output" />
18 </stdio> 19 </outputs>
19 20 <tests>
20 <inputs> 21 <!-- Just test that the tool runs and produces vaguely correct output -->
21 <param name="gff_file" type="data" format="gff3" label="Augustus Generated gff3 File" /> 22 <test>
22 <param name="coords" type="boolean" label="Write genomic coordinates" help="" truevalue="--info" falsevalue="" /> 23 <param name="gff_file" value="augustus_sample.gff" format="gff3"/>
23 </inputs> 24 <output name="output" file="augustus_sample.fasta" format="fasta"/>
24 25 </test>
25 <outputs> 26 </tests>
26 <data format="fasta" name="output" />
27 </outputs>
28
29 <tests>
30 <!-- Just test that the tool runs and produces vaguely correct output -->
31 <test>
32 <param name="gff_file" value="augustus_sample.gff" format="gff3"/>
33 <output name="output" file="augustus_sample.fasta" format="fasta"/>
34 </test>
35 </tests>
36
37
38 <help> 27 <help>
39 28
40 **What it does** 29 **What it does**
41 30
42 Extract proteins from gff3 and encode genomic coordinates in the fasta header. 31 Extract proteins from gff3 and encode genomic coordinates in the fasta header.
43 Currently this only works with gff3 generated using the Augustus gene finder 32 Currently this only works with gff3 generated using the Augustus gene finder
44 33
45 ----
46
47 **References**
48
49
50 </help> 34 </help>
51
52 </tool> 35 </tool>