Mercurial > repos > iuc > mitos2
annotate macros.xml @ 7:b815ec682418 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit dfe519563a762fc72953e4754f76effe5e16cfec
author | iuc |
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date | Tue, 06 Feb 2024 12:36:49 +0000 |
parents | e95d52d295d7 |
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dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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1 <macros> |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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2 <token name="@COMMON_HELP@"> |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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3 <![CDATA[ |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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4 @MITOS_NAME@ does a de-novo annotation of a given metazoan mitochondrial sequence. |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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5 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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6 **Inputs** |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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7 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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8 - A fasta formatted sequence |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
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9 |
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e95d52d295d7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 2d87b0b9c2491ed6fc611b6820b5ebea1d6def23
iuc
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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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dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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11 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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12 - The correct genetic code needs to be selected |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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13 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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14 - Reference data needs to be selected (can be provided by an administrator using the MITOS data manager) |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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15 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
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16 **Outputs** |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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17 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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18 By default the annotation in BED format. Several other outputs can be enabled: |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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19 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
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20 - The annotation can be given as well in GFF, SEQ, or mito (a custom tabular format) |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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21 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
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22 - zipped raw data (all files computed during the run, e.g. BLAST and cmsearch outputs) |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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23 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
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24 - protein and ncRNA prediction plots visualize the predicted genes and their qualities |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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25 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
parents:
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26 - ncRNA structure plots (secondary structures of the predicted ncRNAs) |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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27 |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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28 See http://mitos.bioinf.uni-leipzig.de/help.py |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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29 |
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80323066acd4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
iuc
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30 Contact mitos (at) bioinf (dash) uni (dash) leipzig (dot) de in case of problems. |
80323066acd4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 84c175ed516a3b0074ca06d6546b76f1cbc4fb68"
iuc
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31 |
0
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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32 ]]></token> |
dd589aa77943
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2"
iuc
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33 </macros> |