Mercurial > repos > iuc > jbrowse
annotate jbrowse-fromdir.xml @ 12:db5fe5a3176a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
| author | iuc |
|---|---|
| date | Mon, 06 Feb 2017 12:52:09 -0500 |
| parents | ad4b9d7eae6a |
| children | 5f70e7fe6077 |
| rev | line source |
|---|---|
|
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
3
diff
changeset
|
1 <tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="@WRAPPER_VERSION@"> |
| 3 | 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 <command><![CDATA[ | |
| 9 ## Create output directory | |
| 10 mkdir -p $output.files_path && | |
| 11 ## Copy in jbrowse | |
| 12 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ && | |
| 13 | |
| 14 ## Copy in data directory | |
| 15 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ && | |
| 16 mv $output.files_path/index.html $output | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param label="JBrowse Data Directory" | |
| 20 name="input" | |
| 21 type="data" | |
| 22 help="Look for datasets with 'JBrowse ... Data Directory' in the name" | |
| 23 format="html" /> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/> | |
| 27 </outputs> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
3
diff
changeset
|
28 <tests> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
3
diff
changeset
|
29 </tests> |
| 3 | 30 <help><![CDATA[ |
| 31 Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance. | |
| 32 | |
| 33 @ATTRIBUTION@ | |
| 34 ]]></help> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
3
diff
changeset
|
35 <expand macro="citations"/> |
| 3 | 36 </tool> |