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1 <tool id="CloudMap Config" name="Generate a species configuration file">
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2 <description>for use with CloudMap.</description>
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3 <requirements>
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4 <requirement type="package" version="3.4.1">python3</requirement>
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5 <requirement type="package" version="0.1.3_9af04e0e9125">MiModD</requirement>
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6 </requirements>
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7 <command>
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8 mimodd cm_seqdict $ifile -o $outputfile
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9 </command>
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10
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11 <inputs>
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12 <param name="ifile" type="data" format="vcf" label="vcf input file" />
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13 </inputs>
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14
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15 <outputs>
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16 <data name="outputfile" format="tabular" label="Sequence Dictionary for CloudMap from ${on_string}"/>
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17 </outputs>
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18
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19 <help>
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20 .. class:: infomark
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21
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22 **What it does**
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23
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24 The purpose of this tool is solely to provide compatibility with the external **CloudMap** *Variant Discovery Mapping* and *Hawaiian Variant Mapping* tools.
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25
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26 From a VCF file, the tool extracts the chromosome names and sizes and reports them in the **CloudMap** *species configuration file* format.
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27 Such a file is required as input to the **CloudMap** mapping tools, if you are working with a species other than the natively supported ones (i.e., other than C.elegans or A. thaliana for the current version of CloudMap).
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28
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29 </help>
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30 </tool>
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