annotate tidecluster_reannotate.xml @ 2:299f14a6050a draft

planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
author petr-novak
date Thu, 17 Aug 2023 14:23:02 +0000
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children 9e77d3afefdd
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299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
parents:
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1 <tool id="tc_reannotate" name="TideCluster Reannotate" version="@TOOL_VERSION">
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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2 <macros>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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3 <import>macros.xml</import>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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4 </macros>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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5 <description>Reannotate tandem repeats using similarity-based approach</description>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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6 <expand macro="requirements" />
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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7 <command detect_errors="exit_code"><![CDATA[
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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8 tc_reannotate.py
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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9 -s '$ref_seq'
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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10 -f '$fasta_file'
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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11 -c \${GALAXY_SLOTS:-1}
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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12 -o '$output'
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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13 ]]></command>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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14 <inputs>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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15 <param type="data" name="ref_seq" format="fasta" label="Reference sequence" help="FASTA file to be annotated by TRC library"/>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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16 <param type="data" name="fasta_file" format="fasta" label="Tandem repeat library" help="FASTA file with tandem repeat library from TideCluster"/>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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17 </inputs>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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18 <outputs>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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19 <data name="output" format="gff3" label="${tool.name} on ${on_string}: GFF3 Output"/>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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20 </outputs>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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21 <help><![CDATA[
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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22 This is a tool for reannotating tandem repeats using a similarity-based approach. This tool runs RepeatMasker using the tandem repeat
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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23 library generated by TAREAN in TideCluster. Resulting RepeatMasker output is processed to retain only high-quality tandem repeat hits.
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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24 Overlapping tandem repeat annotation are merged, and regions shorter than twice the monomer length are excluded from the output.
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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25 Reannotate tandem repeats using similarity-based approach can fill in gaps in annotation provided by TideCluster/TideHunter.
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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26 ]]></help>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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27 <citations>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
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28 <!-- Add citations here -->
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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29 </citations>
299f14a6050a planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 65066fa2cd844c8ae882c4ba9bc4e124eada8ffd
petr-novak
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30 </tool>