Mercurial > repos > ntino-krampis > viralcloud

annotate viral_assembly_annotation/viral_assembly.xml @ 0:beaf42837914 draft

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viral cloud resource galaxy tool definitions initial commit
author ntino-krampis
date Thu, 31 Jan 2013 13:41:35 -0500
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beaf42837914 viral cloud resource galaxy tool definitions initial commit
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1 <tool id="vir_assembly" name="Viral Assembly" version="1.0.0">
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2 <description>Run Viral assembly</description>
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3 <command interpreter="python">
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4 viral_assembly.py $input_454 $input_Sanger $input_Solexa $input_Solexa_tp $database $output_Fasta
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5 </command>
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6 <inputs>
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7 <param name="input_454" label="454 reads" type="data" format="sff" optional="true"/>
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8 <param name="input_Sanger" label="Sanger reads" type="data" format="fasta" optional="true" />
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9 <param name="input_Solexa" label="Solexa reads" type="data" format="fastq" optional="true"/>
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10 <param name="input_Solexa_tp" label="Solexa trimpoints" type="data" format="tabular" optional="true"/>
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11 <param name="database" label="Viral database" type="select">
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12 <option value="barda">barda</option>
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13 <option value="giv">giv</option>
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14 <option value="giv3">giv3</option>
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15 <option value="piv">piv</option>
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16 <option value="swiv">swiv</option>
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17 <option value="rtv">rtv</option>
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18 <option value="gcv">gcv</option>
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19 <option value="veev">veev</option>
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20 <option value="hadv">hadv</option>
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21 <option value="mpv">mpv</option>
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22 <option value="norv">norv</option>
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23 <option value="vzv">vzv</option>
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24 <option value="rsv">rsv</option>
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25 <option value="jev">jev</option>
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26 <option value="yfv">yfv</option>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data format="fasta" name="output_Fasta" label="${tool.name} on ${on_string}" />
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31 </outputs>
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32 <help>
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33
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34 **What it does**
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35
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36 This tool uses vir-assembly-pipeline.sh to run viral assembly and consensus sequence generation on the input sequence data.
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37 </help>
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38 </tool>