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annotate augustus_training.xml @ 2:0e9e17d6364e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit c659b84bf74f5abb260ee49ce76b61e5d5fa29c1
author iuc
date Thu, 30 May 2019 06:57:33 -0400
parents 2c4b780eb9f9
children 7d3fa213c3d3
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101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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1 <?xml version="1.0"?>
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2c4b780eb9f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
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2 <tool id="augustus_training" name="Train Augustus" profile="16.04" version="@VERSION@+galaxy2">
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101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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3 <description>ab-initio gene predictor</description>
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4 <macros>
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5 <import>macros.xml</import>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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6 </macros>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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7 <expand macro="requirements">
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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8 <requirement type="package" version="2.31.10">maker</requirement>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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9 </expand>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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10 <command><![CDATA[
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0e9e17d6364e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit c659b84bf74f5abb260ee49ce76b61e5d5fa29c1
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11 cp -r `which augustus | xargs dirname`/../config/ augustus_dir/ &&
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101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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12
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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13 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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15 maker2zff '${maker_gff}' &&
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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17 zff2gff3.pl genome.ann | perl -plne 's/\t(\S+)$/\t\.\t$1/' > genome.gff3 &&
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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19 autoAugTrain.pl --genome=${genome} --species=local --trainingset=genome.gff3 -v &&
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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21 cd 'augustus_dir/species/' && tar cvfz '${output_tar}' 'local'
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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22 ]]></command>
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23 <inputs>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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24 <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
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25 <param name="maker_gff" type="data" format="gff" label="Annotation to use for training"/>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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26 </inputs>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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27 <outputs>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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28 <data name="output_tar" format="augustus" label="${tool.name} on ${on_string}: Augustus trained model"/>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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29 </outputs>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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30 <tests>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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31 <test expect_failure="true">
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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32 <param name="genome" value="human_augustus.fa"/>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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33 <param name="maker_gff" value="annot.gff3"/>
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34 <assert_stderr>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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35 <has_text text="Number of training genes is with 2 too low (at least 100 genes required)" />
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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36 </assert_stderr>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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37 </test>
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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38 </tests>
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39 <help><![CDATA[
101933e63fa8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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40 This tool allows to train Augustus (the ab-initio gene predictor) based on a previous prediction (e.g. made with Maker).
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41 ]]></help>
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42 <expand macro="citations"/>
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43 </tool>