Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder

annotate data_manager/rnastar_index_builder.xml @ 12:a42dbab7917c draft

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planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 599e0c3b37869cc016156f7058e16d6c268bc703
author sanbi-uwc
date Mon, 15 Feb 2016 06:55:55 -0500
parents 6096741e8d83
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2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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1 <?xml version="1.0" encoding="UTF-8" ?>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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2 <tool id="rnastar_index_builder" name="RNA STAR index" tool_type="manage_data" version="0.0.1">
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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3 <description>Build an index for use by the RNA STAR mapping tool</description>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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4 <requirements>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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5 <requirement type="package" version="2.4.0d">rnastar</requirement>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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6 </requirements>
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6096741e8d83 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit e1dfc6180dbf3ae2843b1837a0a07c8ba8b3f314
sanbi-uwc
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7 <command interpreter="python">rnastar_index_builder.py "${out_file}" --fasta_filename "${input1.fields.path}" --fasta_dbkey "${input1.fields.dbkey}" --fasta_description "${input1.fields.name}" --data_table_name "rnastar_index"</command>
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2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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8 <inputs>
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9d6c9d4bc794 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 8a1bc55e1e7846fb7c1cbcef441369cd7f582558
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9 <param name="input1" type="select" label="Genome to index(FASTA format)">
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sanbi-uwc
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10 <options from_data_table="all_fasta"/>
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2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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11 </param>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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12 <param type="text" name="sequence_name" value="" label="Name of sequence" />
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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13 <param type="text" name="sequence_id" value="" label="ID for sequence" />
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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14 </inputs>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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15 <outputs>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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16 <data name="out_file" format="data_manager_json" />
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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17 </outputs>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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18 <help>Help!</help>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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19 <citations><citation></citation>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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20 </citations>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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21 <tests>
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23 </tests>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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24 </tool>