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1 <?xml version="1.0"?>
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2 <tool id="featurecounts_gxfloader" name="featurecounts" tool_type="manage_data" version="1.0.1">
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3 <description>GFF/GTF loader</description>
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4 <requirements>
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5 <requirement type="package" version="1.4.6.p5">featurecounts</requirement>
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6 <requirement type="set_environment">FCOUNT_SCRIPT_PATH</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code description="Error" level="fatal" range="1:" />
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10 </stdio>
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11 <!-- <version_command>kraken -version | awk '{print $NF}'</version_command> -->
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12 <command>
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13 <![CDATA[
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14 mkdir featurecount_gxf && cp "$gxf" featurecount_gxf/ &&
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15 cd .. && python \$FCOUNT_SCRIPT_PATH/data_manager/make_json.py --dbkey "${dbkey}" --provider "${provider}" --ref "${ref}"--out "${out_file}"
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16 ]]>
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17 </command>
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18 <inputs>
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19 <param label="Name for this GFF/GTF" name="dbkey" type="text" />
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20 <param label="Provider for this GFF/GTF" name="provider" type="text" />
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21 <param label="Reference URL for this GFF/GTF" name="ref" type="text" />
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22 <param format="gff,gtf,tabular" label="Select history item" multiple="True" name="gxf" type="data" />
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23 </inputs>
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24 <outputs>
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25 <data format="data_manager_json" name="out_file" />
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26 </outputs>
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27
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28 </tool>
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