Mercurial > repos > dave > data_manager_fetch_index_maf
annotate data_manager/data_manager_fetch_and_index_maf.xml @ 1:edf39ed96bc3 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit f8a19615cd097290a1239d4bb6b8eb52c9d73b03-dirty"
author | dave |
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date | Wed, 15 Jul 2020 15:50:54 -0400 |
parents | de73b258a601 |
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edf39ed96bc3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit f8a19615cd097290a1239d4bb6b8eb52c9d73b03-dirty"
dave
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1 <tool id="data_manager_fetch_and_index_maf" name="Fetch and index" version="1.1.0" tool_type="manage_data" profile="19.01"> |
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de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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2 <description>multiple alignments from UCSC</description> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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3 <requirements> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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4 <requirement type="package" version="3.7">python</requirement> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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5 <requirement type="package" version="0.8.8">bx-python</requirement> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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6 </requirements> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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7 <command detect_errors="exit_code"><![CDATA[ |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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8 python '$__tool_directory__/data_manager_fetch_and_index_maf.py' --nexus '$nexus' |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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9 --name '$name' --output '$output' --dbkey '${dbkey.fields.dbkey}' |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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10 ]]></command> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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11 <inputs> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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12 <param name="dbkey" type="select" label="Species aligned against"> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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13 <options from_data_table="all_fasta"/> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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14 </param> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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15 <param name="nexus" type="text" label="FTP path to nexus file on UCSC." help="The MAF paths will be computed from this" /> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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16 <param name="name" type="text" label="Display name for this multi-alignment" /> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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17 </inputs> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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18 <outputs> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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19 <data name="output" format="data_manager_json" metadata_source="dbkey" /> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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20 </outputs> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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21 <help> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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22 **What it does** |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
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23 |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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24 This data manager fetches a multiple alignment from UCSC's FTP server and indexes it with bx-python. |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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25 </help> |
de73b258a601
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_fetch_index_maf commit 21852ee28cf191d12b1ffe5583efaa5deeb1d80d-dirty"
dave
parents:
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26 </tool> |