Mercurial > repos > sanbi-uwc > data_manager_fetch_refseq

annotate data_manager_conf.xml @ 8:97bf61f2fdae draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty
author sanbi-uwc
date Fri, 07 Sep 2018 19:52:24 -0400
parents efdead58e937
children dd9f976e9d97
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
1 <?xml version="1.0"?>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
2 <data_managers>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
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
parents:
diff changeset
4 <data_table name="all_fasta">
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
5 <output>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
6 <column name="value" />
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
7 <column name="dbkey" />
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
8 <column name="name" />
4
efe0f451c40f planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty
sanbi-uwc
parents: 0
diff changeset
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
parents:
diff changeset
10 <move type="file">
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
11 <source>${path}</source>
8
97bf61f2fdae planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty
sanbi-uwc
parents: 7
diff changeset
12 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">refseq/${dbkey}/${value}.fasta</target>
0
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
13 </move>
8
97bf61f2fdae planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit b682adad2c3c74567d23e1a5cf2bfcc3df1c96ae-dirty
sanbi-uwc
parents: 7
diff changeset
14 <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
parents:
diff changeset
15 <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
parents:
diff changeset
16 </column>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
17 </output>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
18 </data_table>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
19 </data_manager>
cfe6cd521835 planemo upload for repository https://github.com/pvanheus/refseq_fasta_data_manager commit cfd2aa18826b938402ccfc6003f1793886001202-dirty
sanbi-uwc
parents:
diff changeset
20 </data_managers>