Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder

annotate data_manager/rnastar_index_builder.xml @ 4:9d6c9d4bc794 draft

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planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 8a1bc55e1e7846fb7c1cbcef441369cd7f582558
author sanbi-uwc
date Wed, 10 Feb 2016 02:26:15 -0500
parents d00829775046
children 819e34a14f18
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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" ?>
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2 <tool id="rnastar_index_builder" name="RNA STAR index" tool_type="manage_data" version="0.0.1">
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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
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4 <requirements>
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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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d00829775046 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit ff1ec11f4bc440e971ce083c444fffaa964527d7
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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_indexes"</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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10 <option from_data_table="all_fasta"/>
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
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13 <param type="text" name="sequence_id" value="" label="ID for sequence" />
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14 <!--<conditional name="advanced_options">-->
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15 <!--<param name="show_advanced_options" type="boolean" label="Show advanced options?"-->
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16 <!--truevalue="yes" falsevalue="no" checked="false" />-->
316b24a15236 planemo upload for repository https://github.com/pvanheus/data_manager_rnastar_index_builder commit 265fa1966ea606ebccea8c2865043c014959c10c-dirty
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17 <!--<when value="yes">-->
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18 <!--<param name="chr_bin_nbits" type="integer" label="Scale of chromosome bins"-->
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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" />-->
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20 <!--</when>-->
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21 <!--<when value="no" />-->
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22 <!--</conditional>-->
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23 </inputs>
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24 <outputs>
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25 <!-- <data from_work_dir="tempstargenomedir" auto_format="false"></data>-->
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26 <data name="out_file" format="data_manager_json" />
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27 </outputs>
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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>
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30 </citations>
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31 <tests>
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32
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33 </tests>
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34 </tool>