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comparison jbrowse-fromdir.xml @ 3:7342f467507b draft

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Uploaded v0.4 of JBrowse
author iuc
date Thu, 31 Dec 2015 13:58:43 -0500
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children ad4b9d7eae6a
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2:b6a0e126dbee 3:7342f467507b
1 <tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="0.4">
2 <description>upgrades the bare data directory to a full JBrowse instance</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <version_command>python jbrowse.py --version</version_command>
9 <command><![CDATA[
10 ## Create output directory
11 mkdir -p $output.files_path &&
12 ## Copy in jbrowse
13 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ &&
14
15 ## Copy in data directory
16 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ &&
17 mv $output.files_path/index.html $output
18 ]]></command>
19 <inputs>
20 <param label="JBrowse Data Directory"
21 name="input"
22 type="data"
23 help="Look for datasets with 'JBrowse ... Data Directory' in the name"
24 format="html" />
25 </inputs>
26 <outputs>
27 <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/>
28 </outputs>
29 <help><![CDATA[
30 Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance.
31
32 @ATTRIBUTION@
33 ]]></help>
34 <tests>
35 </tests>
36 <citations>
37 <citation type="doi">10.1101/gr.094607.109</citation>
38 </citations>
39 </tool>
40