Mercurial > repos > iuc > maker_map_ids

annotate map_ids.xml @ 7:e906fa778440 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 739da8be15072cfd98cc0b8d6bfa9dedb25a98f0"
author iuc
date Tue, 08 Feb 2022 14:18:25 +0000
parents 060ea7339911
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060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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1 <?xml version="1.0"?>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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2 <tool id="maker_map_ids" name="Map annotation ids" profile="16.04" version="@VERSION@">
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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3 <description>on a Maker annotation</description>
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e906fa778440 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 739da8be15072cfd98cc0b8d6bfa9dedb25a98f0"
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4 <xrefs>
e906fa778440 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 739da8be15072cfd98cc0b8d6bfa9dedb25a98f0"
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5 <xref type="bio.tools">maker</xref>
e906fa778440 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 739da8be15072cfd98cc0b8d6bfa9dedb25a98f0"
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6 </xrefs>
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060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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7 <macros>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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8 <import>macros.xml</import>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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9 </macros>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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10 <expand macro="requirements"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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11 <command><![CDATA[
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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12 cp '${maker_gff}' '${renamed}' &&
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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13 maker_map_ids --prefix '${prefix}' --justify ${justify} '${maker_gff}' > '${id_map}' &&
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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14 map_gff_ids '${id_map}' '${renamed}'
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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15 ]]></command>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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16 <inputs>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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17 <param name="maker_gff" type="data" format="gff" label="Maker annotation where to change ids"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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18 <param name="prefix" type="text" label="Prefix for ids"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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19 <param name="justify" type="integer" value="6" min="2" max="20" label="Justify numeric ids to this length"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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20 </inputs>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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21 <outputs>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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22 <data format="gff" name="renamed" label="${tool.name} on ${on_string}: renamed GFF"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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23 <data format="tabular" name="id_map" label="${tool.name} on ${on_string}: ID map"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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24 </outputs>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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25 <tests>
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26 <test>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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27 <param name="maker_gff" value="annot.gff3"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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28 <param name="prefix" value="YES"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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29 <param name="justify" value="6"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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30 <output name="renamed" file="annot_mapped.gff3"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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31 <output name="id_map" file="id_map.tsv"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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32 </test>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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33 </tests>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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34 <help><![CDATA[
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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35 MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKER's inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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37 This tool will automatically assign new ids to a Maker annotation respecting a specified pattern.
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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39 .. _Maker: http://www.yandell-lab.org/software/maker.html
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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40 ]]></help>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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41 <expand macro="citations"/>
060ea7339911 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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42 </tool>