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annotate data_manager/rnastar_index_builder.xml @ 0:2883a3b7dc56 draft

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planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
author sanbi-uwc
date Mon, 08 Feb 2016 03:23:34 -0500
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children 316b24a15236
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2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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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
sanbi-uwc
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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>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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7 <command interpreter="python">bwa_index_builder.py "${out_file}" --fasta_filename "${input1.fields.path}" --fasta_dbkey "${input1.fields.dbkey}" --fasta_description "${input1.fields.name}" --data_table_name "rnastar_indexes"</command>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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8 <inputs>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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9 <param name="input1" type="data" format="fasta" label="Genome to index(FASTA format)">
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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10 <option from_data_table="all_fasta"/>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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11 </param>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
sanbi-uwc
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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
sanbi-uwc
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14 <conditional name="advanced_options">
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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15 <param name="show_advanced_options" type="boolean" label="Show advanced options?"
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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16 truevalue="yes" falsevalue="no" checked="false" />
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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17 <when value="yes">
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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18 <param name="chr_bin_nbits" type="integer" label="Scale of chromosome bins"
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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19 help="value is log2(chrBin), where chrBin is the size of the bins for genome storage: each chromosome will occupy an integer number of bins" default="18" />
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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20 </when>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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21 <when value="no" />
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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22 </conditional>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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23 </inputs>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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24 <outputs>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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25 <!-- <data from_work_dir="tempstargenomedir" auto_format="false"></data>-->
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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26 <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
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27 </outputs>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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28 <help>Help!</help>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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29 <citations><citation></citation>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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30 </citations>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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31 <tests>
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32
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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33 </tests>
2883a3b7dc56 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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34 </tool>