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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author iuc
date Thu, 19 Oct 2017 15:23:15 -0400
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-1:000000000000 0:460688f223f4
1 <?xml version="1.0"?>
2 <tool id="augustus_training" name="Train Augustus" profile="16.04" version="@VERSION@">
3 <description>ab-initio gene predictor</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements">
8 <requirement type="package" version="2.31.9">maker</requirement>
9 </expand>
10 <command><![CDATA[
11 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
12
13 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
14
15 maker2zff '${maker_gff}' &&
16
17 zff2gff3.pl genome.ann | perl -plne 's/\t(\S+)$/\t\.\t$1/' > genome.gff3 &&
18
19 autoAugTrain.pl --genome=${genome} --species=local --trainingset=genome.gff3 -v &&
20
21 cd 'augustus_dir/species/' && tar cvfz '${output_tar}' 'local'
22 ]]></command>
23 <inputs>
24 <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
25 <param name="maker_gff" type="data" format="gff" label="Annotation to use for training"/>
26 </inputs>
27 <outputs>
28 <data name="output_tar" format="augustus" label="${tool.name} on ${on_string}: Augustus trained model"/>
29 </outputs>
30 <tests>
31 <test expect_failure="true">
32 <param name="genome" value="human_augustus.fa"/>
33 <param name="maker_gff" value="annot.gff3"/>
34 <assert_stderr>
35 <has_text text="Number of training genes is with 2 too low (at least 100 genes required)" />
36 </assert_stderr>
37 </test>
38 </tests>
39 <help><![CDATA[
40 This tool allows to train Augustus (the ab-initio gene predictor) based on a previous prediction (e.g. made with Maker).
41 ]]></help>
42 <expand macro="citations"/>
43 </tool>