Mercurial > repos > iuc > maker_map_ids

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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 14:16:53 +0000
parents b9735b183d75
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4c6b56ad043a 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"?>
4c6b56ad043a 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@">
4c6b56ad043a 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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b9735b183d75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <xrefs>
b9735b183d75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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5 <xref type="bio.tools">maker</xref>
b9735b183d75 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 </xrefs>
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4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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7 <macros>
4c6b56ad043a 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>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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9 </macros>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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10 <expand macro="requirements"/>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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11 <command><![CDATA[
4c6b56ad043a 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}' &&
4c6b56ad043a 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}' > '${id_map}' &&
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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14 map_gff_ids '${id_map}' '${renamed}'
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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15 ]]></command>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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16 <inputs>
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17 <param name="maker_gff" type="data" format="gff" label="Maker annotation where to change ids"/>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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18 <param name="prefix" type="text" label="Prefix for ids"/>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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19 <param name="justify" type="integer" value="6" min="2" max="20" label="Justify numeric ids to this length"/>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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20 </inputs>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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21 <outputs>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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22 <data format="gff" name="renamed" label="${tool.name} on ${on_string}: renamed GFF"/>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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23 <data format="tabular" name="id_map" label="${tool.name} on ${on_string}: ID map"/>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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24 </outputs>
4c6b56ad043a 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>
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27 <param name="maker_gff" value="annot.gff3"/>
4c6b56ad043a 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"/>
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29 <param name="justify" value="6"/>
4c6b56ad043a 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"/>
4c6b56ad043a 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"/>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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32 </test>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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33 </tests>
4c6b56ad043a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 2896dcfd180800d00ea413a59264ef8b11788b8e
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34 <help><![CDATA[
4c6b56ad043a 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.
4c6b56ad043a 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.
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39 .. _Maker: http://www.yandell-lab.org/software/maker.html
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40 ]]></help>
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41 <expand macro="citations"/>
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42 </tool>