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1 <tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="0.4">
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2 <description>upgrades the bare data directory to a full JBrowse instance</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <version_command>python jbrowse.py --version</version_command>
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9 <command><![CDATA[
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10 ## Create output directory
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11 mkdir -p $output.files_path &&
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12 ## Copy in jbrowse
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13 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&
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14
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15 ## Copy in data directory
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16 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
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17 mv $output.files_path/index.html $output
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18 ]]></command>
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19 <inputs>
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20 <param label="JBrowse Data Directory"
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21 name="input"
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22 type="data"
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23 help="Look for datasets with 'JBrowse ... Data Directory' in the name"
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24 format="html" />
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25 </inputs>
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26 <outputs>
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27 <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/>
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28 </outputs>
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29 <help><![CDATA[
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30 Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance.
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31
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32 @ATTRIBUTION@
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33 ]]></help>
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34 <tests>
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35 </tests>
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36 <citations>
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37 <citation type="doi">10.1101/gr.094607.109</citation>
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38 </citations>
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39 </tool>
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40
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