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annotate jbrowse-fromdir.xml @ 42:6cd09d7b5f37 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
author iuc
date Sat, 06 Feb 2021 12:01:13 +0000
parents 8774b28235bb
children
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5f70e7fe6077 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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1 <tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="@TOOL_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 <edam_operations>
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7 <edam_operation>operation_3434</edam_operation>
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8 </edam_operations>
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9 <edam_topics>
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10 <edam_topic>topic_3307</edam_topic>
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11 <edam_topic>topic_0092</edam_topic>
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12 </edam_topics>
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13 <expand macro="requirements"/>
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14 <command detect_errors="exit_code"><![CDATA[
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15 ## Create output directory
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16 mkdir -p $output.files_path &&
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18 export JBROWSE_SOURCE_DIR=\$(dirname \$(command -v prepare-refseqs.pl))/../opt/jbrowse &&
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19
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20 ## Copy in jbrowse
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21 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&
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22
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23 ## Copy in data directory
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24 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
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25 cp $output.files_path/index.html $output
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26 ]]></command>
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27 <inputs>
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28 <param label="JBrowse Data Directory"
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29 name="input"
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30 type="data"
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31 help="Look for datasets with 'JBrowse ... Data Directory' in the name"
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32 format="html" />
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33 </inputs>
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34 <outputs>
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35 <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/>
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36 </outputs>
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37 <tests>
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38 </tests>
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39 <help><![CDATA[
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40 Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance.
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41
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42 @ATTRIBUTION@
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43 ]]></help>
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44 <expand macro="citations"/>
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45 </tool>