Mercurial > repos > iuc > jbrowse
annotate jbrowse-fromdir.xml @ 31:2bb2e07a7a21 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
| author | iuc |
|---|---|
| date | Mon, 15 Apr 2019 10:31:26 -0400 |
| parents | 1cfc579079a6 |
| children | 3235aeb45c22 |
| rev | line source |
|---|---|
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5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
parents:
8
diff
changeset
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1 <tool id="jbrowse_to_standalone" name="JBrowse - Data Directory to Standalone" version="@TOOL_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"/> | |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
22
diff
changeset
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7 <command detect_errors="exit_code"><![CDATA[ |
| 3 | 8 ## Create output directory |
| 9 mkdir -p $output.files_path && | |
| 10 ## Copy in jbrowse | |
| 11 cp -R \${JBROWSE_SOURCE_DIR}/* $output.files_path/ && | |
| 12 | |
| 13 ## Copy in data directory | |
| 14 cp -R $input.dataset.extra_files_path/data/ $output.files_path/ && | |
| 15 mv $output.files_path/index.html $output | |
| 16 ]]></command> | |
| 17 <inputs> | |
| 18 <param label="JBrowse Data Directory" | |
| 19 name="input" | |
| 20 type="data" | |
| 21 help="Look for datasets with 'JBrowse ... Data Directory' in the name" | |
| 22 format="html" /> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data format="html" name="output" label="#set $name = $input.name.replace('Data Directory', 'Standalone')# $name"/> | |
| 26 </outputs> | |
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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
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27 <tests> |
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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
|
28 </tests> |
| 3 | 29 <help><![CDATA[ |
| 30 Upgrades an existing bare JBrowse "data" directory into a full-fledged JBrowse instance. | |
| 31 | |
| 32 @ATTRIBUTION@ | |
| 33 ]]></help> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
3
diff
changeset
|
34 <expand macro="citations"/> |
| 3 | 35 </tool> |