Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq

annotate data_manager_conf.xml @ 16:d10b5e0ed486 draft

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planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
author sanbi-uwc
date Sat, 08 Sep 2018 04:19:52 -0400
parents 01ea53470921
children 0347d4d8b436
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cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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1 <?xml version="1.0"?>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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2 <data_managers>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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3 <data_manager tool_file="data_manager/fetch_refseq.xml" id="fetch_genome_fetch_refseq">
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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4 <data_table name="all_fasta">
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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5 <output>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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6 <column name="value" />
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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7 <column name="dbkey" />
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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8 <column name="name" />
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efe0f451c40f planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty
sanbi-uwc
parents: 0
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9 <column name="path" output_ref="output_file" >
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cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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10 <move type="file">
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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11 <source>${path}</source>
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dd9f976e9d97 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
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12 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}"><![CDATA[
14
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sanbi-uwc
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13 #set name_parts = str($dbkey).split('.')
1977080c99ec planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 13
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14 #if len($name_parts) == 3:
1977080c99ec planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 13
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15 #set release_num = $name_parts[1]
1977080c99ec planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 13
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16 #else
1977080c99ec planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 13
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17 #set release_num = 'UNKNOWN_RELEASE'
15
01ea53470921 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
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18 #end if
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dd9f976e9d97 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 8
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19 refseq/${release_num}/${value}.fasta
dd9f976e9d97 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 8
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20 ]]></target>
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cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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21 </move>
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d10b5e0ed486 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 15
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22 <value_translation><![CDATA[
d10b5e0ed486 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 15
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23 #set name_parts = str($dbkey).split('.')
d10b5e0ed486 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 15
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24 #if len($name_parts) == 3:
d10b5e0ed486 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 15
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25 #set release_num = $name_parts[1]
d10b5e0ed486 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 15
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26 #else
d10b5e0ed486 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 15
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27 #set release_num = 'UNKNOWN_RELEASE'
d10b5e0ed486 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 15
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28 #end if
d10b5e0ed486 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 15
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29 refseq/${release_num}/${value}.fasta
d10b5e0ed486 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents: 15
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30 ]]></value_translation>
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cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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31 <value_translation type="function">abspath</value_translation>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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32 </column>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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33 </output>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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34 </data_table>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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35 </data_manager>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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36 </data_managers>