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annotate snap_training.xml @ 0:821bf8bc5623 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author iuc
date Fri, 20 Oct 2017 03:51:58 -0400
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821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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1 <?xml version="1.0"?>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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2 <tool id="snap_training" name="Train SNAP" profile="16.04" version="@VERSION@">
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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3 <description>ab-initio gene predictor</description>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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4 <macros>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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5 <import>macros.xml</import>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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6 </macros>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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7 <expand macro="requirements">
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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8 <requirement type="package" version="2.31.9">maker</requirement>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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9 </expand>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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10 <command><![CDATA[
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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11 cp '${maker_gff}' input.gff3 &&
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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12 echo "\##FASTA" >> input.gff3 &&
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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13 cat '${genome}' >> input.gff3 &&
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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14 maker2zff input.gff3 &&
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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15 fathom -categorize ${gene_num} genome.ann genome.dna &&
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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16 fathom -export ${gene_num} -plus uni.ann uni.dna &&
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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17 forge export.ann export.dna &&
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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18 hmm-assembler.pl snap_training . > '${output}'
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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19 ]]></command>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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20 <inputs>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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21 <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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22 <param name="maker_gff" type="data" format="gff" label="Maker annotation to use for training"/>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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23 <param name="gene_num" type="integer" value="1000" label="Number of gene model to use for training"/>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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24 </inputs>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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25 <outputs>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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26 <data format="snaphmm" name="output" label="${tool.name} on ${on_string}: SNAP trained model"/>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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27 </outputs>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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28 <tests>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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29 <test>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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30 <param name="genome" value="human.fa"/>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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31 <param name="maker_gff" value="annot.gff3"/>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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32 <output name="output" compare="sim_size" file="snap.hmm"/>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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33 </test>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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34 </tests>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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35 <help><![CDATA[
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
iuc
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36 This tool allows to train SNAP (an ab-initio gene predictor) based on a previous prediction made with Maker.
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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37 ]]></help>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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38 <expand macro="citations"/>
821bf8bc5623 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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39 </tool>