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1 <tool id="VarAmpliCNV_GC" name="Get Amplicon GC-Content" version="0.1.0" python_template_version="2.7">
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2 <requirements>
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3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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6 getGCAmplicon.py
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7
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8 ## amplicon input file
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9 -a '$input'
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10
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11 ## output file
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12 -o '$gcOut'
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13
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14 ## 2bit reference gene file
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15 -f $index
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16
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17 ]]></command>
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18 <inputs>
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19 <param name="input" type="data" format="bed" optional="false" label="Amplicon Design File (BED)" help="This file is the HaloPlex design file, containing individual amplicons." />
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20 <param name="index" type="select">
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21 <options from_data_table="TwoBitDocker" />
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22 </param>
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23 </inputs>
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24 <outputs>
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25 <data name="gcOut" format="tabular" label="VarAmpliCNV on ${on_string}: GC-content" />
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26 <!--<data name="ampliconOut" format="tabular" label="Amplicon Gene annotations" />-->
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27 </outputs>
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28 <help>
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29 **VarAmpliCNV : GC-calculation**
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30
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31 Calculate the GC-content of entries in a BED file.
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32
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33 **Parameters are :**
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34
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35 * Amplicon Design File (BED) : The de-duplicated amplicon list, generated by "varAmpliCNV Annotate".
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36 * Genome Build : Select a genome build from the configured options to extract GC content from.
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37
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38 **Output files :**
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39
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40 * GC-content (txt) : Tabular file containing GC information per region.
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41
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42 </help>
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43 </tool>
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