Mercurial > repos > sanbi-uwc > data_manager_rnastar_index_builder

<?xml version="1.0" encoding="UTF-8" ?>
<tool id="rnastar_index_builder" name="RNA STAR index" tool_type="manage_data" version="0.0.1">
    <description>Build an index for use by the RNA STAR mapping tool</description>
    <requirements>
        <requirement type="package" version="2.4.0d">rnastar</requirement>
    </requirements>
    <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>
    <inputs>
        <param name="input1" type="data" format="fasta" label="Genome to index(FASTA format)">
            <option from_data_table="all_fasta"/>
        </param>
        <param type="text" name="sequence_name" value="" label="Name of sequence" />
        <param type="text" name="sequence_id" value="" label="ID for sequence" />
        <!--<conditional name="advanced_options">-->
            <!--<param name="show_advanced_options" type="boolean" label="Show advanced options?"-->
                   <!--truevalue="yes" falsevalue="no" checked="false" />-->
            <!--<when value="yes">-->
                <!--<param name="chr_bin_nbits" type="integer" label="Scale of chromosome bins"-->
                       <!--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" />-->
            <!--</when>-->
            <!--<when value="no" />-->
        <!--</conditional>-->
    </inputs>
    <outputs>
        <!-- <data from_work_dir="tempstargenomedir" auto_format="false"></data>-->
        <data name="out_file" format="data_manager_json" />
    </outputs>
    <help>Help!</help>
    <citations><citation></citation>
    </citations>
    <tests>

    </tests>
</tool>
author	sanbi-uwc
date	Mon, 08 Feb 2016 03:50:42 -0500
parents	316b24a15236
children	d00829775046