Mercurial > repos > nate > data_manager_bowtie2_index_builder

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
author nate
date Tue, 29 Jul 2025 17:13:06 +0000
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6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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1 <?xml version="1.0"?>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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2 <data_managers>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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3 <data_manager tool_file="data_manager/bowtie2_index_builder.xml" id="bowtie2_index_builder">
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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4 <data_table name="bowtie2_indexes">
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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5 <output>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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6 <column name="value" />
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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7 <column name="dbkey" />
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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8 <column name="name" />
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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9 <column name="path" output_ref="out_file" >
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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10 <move type="directory" relativize_symlinks="True">
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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11 <!-- <source>${path}</source>--> <!-- out_file.extra_files_path is used as base by default --> <!-- if no source, eg for type=directory, then refers to base -->
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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12 <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">genomes/${dbkey}/bowtie_index/v2/${value}</target>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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13 </move>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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14 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${value}</value_translation>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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15 <value_translation type="function">abspath</value_translation>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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16 </column>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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17 </output>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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18 </data_table>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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19
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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20 <data_table name="tophat2_indexes">
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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21 <output>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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22 <column name="value" />
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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23 <column name="dbkey" />
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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24 <column name="name" />
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
parents:
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25 <column name="path" output_ref="out_file" >
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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26 <!-- no move, always happens as part of bowtie2 and uses that path -->
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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27 <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/genomes/${dbkey}/bowtie_index/v2/${value}/${value}</value_translation>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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28 <value_translation type="function">abspath</value_translation>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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29 </column>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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30 </output>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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31 </data_table>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
nate
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32 </data_manager>
6220ea344019 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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33 </data_managers>