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annotate macros.xml @ 4:c7553ba39670 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
author iuc
date Wed, 01 Mar 2023 22:40:00 +0000
parents 1f4933f5a323
children 8b08ea650060
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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1 <macros>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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2 <token name="@COMMON_HELP@">
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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3 <![CDATA[
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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4 @MITOS_NAME@ does a de-novo annotation of a given metazoan mitochondrial sequence.
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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6 **Inputs**
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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8 - A fasta formatted sequence
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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10 - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection". The resulting collection can then used as input to @MITOS_NAME@.
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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12 - The correct genetic code needs to be selected
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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14 - Reference data needs to be selected (can be provided by an administrator using the MITOS data manager)
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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16 **Outputs**
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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18 By default the annotation in BED format. Several other outputs can be enabled:
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39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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20 - The annotation can be given as well in GFF, SEQ, or mito (a custom tabular format)
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22 - zipped raw data (all files computed during the run, e.g. BLAST and cmsearch outputs)
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24 - protein and ncRNA prediction plots visualize the predicted genes and their qualities
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26 - ncRNA structure plots (secondary structures of the predicted ncRNAs)
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28 See http://mitos.bioinf.uni-leipzig.de/help.py
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30 Contact mitos (at) bioinf (dash) uni (dash) leipzig (dot) de in case of problems.
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32 ]]></token>
39b6485e2d34 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
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33 </macros>