Mercurial > repos > iuc > snap_training

annotate snap_training.xml @ 1:1cd443d67e61 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:38:10 +0000
parents ba3d91ded5db
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ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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1 <?xml version="1.0"?>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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2 <tool id="snap_training" name="Train SNAP" profile="16.04" version="@VERSION@+galaxy1">
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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3 <description>ab-initio gene predictor</description>
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1cd443d67e61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xrefs>
1cd443d67e61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 <xref type="bio.tools">snap</xref>
1cd443d67e61 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 </xrefs>
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ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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7 <macros>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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8 <import>macros.xml</import>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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9 </macros>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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10 <expand macro="requirements">
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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11 <requirement type="package" version="2.31.10">maker</requirement>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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12 </expand>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
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13 <command><![CDATA[
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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14 cp '${maker_gff}' input.gff3 &&
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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15 echo "\##FASTA" >> input.gff3 &&
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
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16 cat '${genome}' >> input.gff3 &&
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
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17 maker2zff input.gff3 &&
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
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18 fathom -categorize ${gene_num} genome.ann genome.dna &&
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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19 fathom -export ${gene_num} -plus uni.ann uni.dna &&
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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20 forge export.ann export.dna &&
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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21 hmm-assembler.pl snap_training . > '${output}'
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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22 ]]></command>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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23 <inputs>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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24 <param name="genome" type="data" format="fasta" label="Genome to annotate"/>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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25 <param name="maker_gff" type="data" format="gff" label="Maker annotation to use for training"/>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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26 <param name="gene_num" type="integer" value="1000" label="Number of gene model to use for training"/>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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27 </inputs>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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28 <outputs>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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29 <data format="snaphmm" name="output" label="${tool.name} on ${on_string}: SNAP trained model"/>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
iuc
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30 </outputs>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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31 <tests>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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32 <test>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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33 <param name="genome" value="human.fa"/>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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34 <param name="maker_gff" value="annot.gff3"/>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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35 <output name="output" compare="sim_size" file="snap.hmm"/>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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36 </test>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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37 </tests>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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38 <help><![CDATA[
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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39 This tool allows to train SNAP (an ab-initio gene predictor) based on a previous prediction made with Maker.
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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40 ]]></help>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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41 <expand macro="citations"/>
ba3d91ded5db planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snap commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
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42 </tool>