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annotate longORF.xml @ 3:7701185ca677 draft default tip

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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 82ae2fa7e7a4a51f7583c6a95bdafc5f843c7c3b
author mbernt
date Mon, 07 Aug 2023 13:52:25 +0000
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7701185ca677 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 82ae2fa7e7a4a51f7583c6a95bdafc5f843c7c3b
mbernt
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1 <tool id="longORF" name="Obtain longest ORFs" version="0.3.0">
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2 <description> in six-frame translations</description>
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3 <command><![CDATA[
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4 python $__tool_directory__/getLongestORF.py $input $output_longestORF $output_ORFs
ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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5 ]]>
ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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6 </command>
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7 <inputs>
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8 <param name="input" format="fasta" type="data" label="sequences"/>
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9 </inputs>
ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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10 <outputs>
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11 <data name="output_longestORF" format="fasta"/>
ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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12 <data name="output_ORFs" format="tabular"/>
ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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13 </outputs>
ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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15 <tests>
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16 <test>
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17 <param name="input" value="test_input.fasta"/>
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18 <output name="output_longestORF" file="test_output.fasta"/>
ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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19 <output name="output_ORFs" file="test_output.tab"/>
ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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20 </test>
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21 </tests>
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22 <help><![CDATA[
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23 **What it does**
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25 This tool identifies the longest Open Reading Frames within the six-frame translations of a set of sequences.
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27 **Input**
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29 It takes an amino acid fasta file with all open reading frames (+ and - strand) listed by the correspondng transcript. The tool is designed to process the output of the Galaxy tool "getorf" from the EMBOSS package.
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31 **Output**
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33 For each transcript, the respected longest ORF is identified and listed in fasta format. Furthermore, table with information about seqID, start, end, length, orientation, longest for all ORFs is given.]]>
ec898924d8c7 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/blob/master/tools/longorf/ commit 8e118a4d24047e2c62912b962e854f789d6ff559
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34 </help>
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35 </tool>