Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq
annotate data_manager_conf.xml @ 14:1977080c99ec draft
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
author | sanbi-uwc |
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date | Sat, 08 Sep 2018 03:24:20 -0400 |
parents | dd9f976e9d97 |
children | 01ea53470921 |
rev | line source |
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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
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9 <column name="path" output_ref="output_file" > |
0
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>${path}</source> |
13
dd9f976e9d97
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents:
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12 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}"><![CDATA[ |
14
1977080c99ec
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents:
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13 #set name_parts = str($dbkey).split('.') |
1977080c99ec
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents:
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14 #if len($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 = $name_parts[1] |
1977080c99ec
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents:
13
diff
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16 #else |
1977080c99ec
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents:
13
diff
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17 #set release_num = 'UNKNOWN_RELEASE' |
1977080c99ec
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents:
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18 #fi |
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dd9f976e9d97
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents:
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19 refseq/${release_num}/${value}.fasta |
dd9f976e9d97
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit 687fed3e6ffed745baf5d6241ee82f2bd9671256-dirty
sanbi-uwc
parents:
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20 ]]></target> |
0
cfe6cd521835
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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21 </move> |
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97bf61f2fdae
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty
sanbi-uwc
parents:
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22 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/refseq/${dbkey}/${value}.fasta</value_translation> |
0
cfe6cd521835
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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23 <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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24 </column> |
cfe6cd521835
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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25 </output> |
cfe6cd521835
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
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26 </data_table> |
cfe6cd521835
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
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27 </data_manager> |
cfe6cd521835
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff
changeset
|
28 </data_managers> |