Mercurial > repos > iuc > kofamscan

annotate tool_data_table_conf.xml.sample @ 5:8ec7636fa875 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit 1e2ca1537bd6d141a3494d6bb0a2f050082f7257
author iuc
date Mon, 06 May 2024 18:37:31 +0000
parents c3c46f14c7a4
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c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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1 <?xml version="1.0"?>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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2 <tables>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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3 <!-- versioned data can be downloaded from
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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4 ftp://ftp.genome.jp/pub/db/kofam/ or https://www.genome.jp/ftp/db/kofam/
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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5 see also https://www.genome.jp/tools/kofamkoala/.
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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6
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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7 the downloads contain ko_list.gz and profiles.tar.gz for each version
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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8 the ko_list entry should point to the file extracted from ko_list.gz
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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9 the profile_dir entry should point to the directory extracted from profiles.tar.gz
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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10
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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11 -->
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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12 <table name="kofam" comment_char="#">
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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13 <columns>value, name, profile_dir, ko_list</columns>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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14 <file path="tool-data/kofam.loc" />
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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15 </table>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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16 <!--
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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17 the profile dir contains many K....hmm files and usually two .hal files
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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18 the .hal files are simple text files listing a set of K files (one per line)
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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19 which allow to specify subsets of K files easily
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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20
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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21 this data table allows to specify these subset files for each entry in
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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22 the kofam datatabe
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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23 - value should be a .hal file in the profiles dir (could also be a K file)
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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24 - name the name shown to the user in the select
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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25 - kofam_value should be equal to the value of the corresoponding entry in kofam
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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26 -->
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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27 <table name="kofam_subset" comment_char="#">
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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28 <columns>value, name, kofam_value</columns>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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29 <file path="tool-data/kofam_subset.loc" />
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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30 </table>
c3c46f14c7a4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kofamscan commit db30370820c68a8add7974d70ad04585cea5b084
iuc
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31 </tables>