annotate jbrowse-fromdir.xml @ 16:b5c5470d7c09 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit c306d242caf7e0447517c9749ca7656823f315e5
author iuc
date Wed, 13 Sep 2017 13:07:20 -0400
parents ad4b9d7eae6a
children 5f70e7fe6077
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ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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1 <tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="@WRAPPER_VERSION@">
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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 <command><![CDATA[
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9 ## Create output directory
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10 mkdir -p $output.files_path &&
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11 ## Copy in jbrowse
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12 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&
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14 ## Copy in data directory
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15 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
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16 mv $output.files_path/index.html $output
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17 ]]></command>
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18 <inputs>
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19 <param label="JBrowse Data Directory"
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20 name="input"
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21 type="data"
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22 help="Look for datasets with 'JBrowse ... Data Directory' in the name"
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23 format="html" />
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24 </inputs>
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25 <outputs>
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26 <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/>
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27 </outputs>
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ad4b9d7eae6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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28 <tests>
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29 </tests>
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30 <help><![CDATA[
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31 Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance.
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32
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33 @ATTRIBUTION@
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34 ]]></help>
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35 <expand macro="citations"/>
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36 </tool>