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annotate snpEff_databases.xml @ 23:924af057bbca draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
author jjohnson
date Sat, 09 Apr 2016 11:51:40 -0400
parents bb0797deab78
children
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36f3c82323e6 Use tool_data_table with key and version columns added to allow for multiple versions in a .loc file
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1 <tool id="snpEff_databases" name="SnpEff Available Databases" version="@WRAPPER_VERSION@.0">
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2 <description></description>
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3 <macros>
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4 <import>snpEff_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 <expand macro="version_command" />
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9 <command>
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10 <![CDATA[
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924af057bbca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 93465571cf180554c3548338a68fa0f1604985dc-dirty
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11 java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > "$snpeff_dbs"
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12 ]]>
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13 </command>
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14 <inputs>
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15 </inputs>
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16 <outputs>
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17 <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" />
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18 </outputs>
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19 <tests>
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20 <test>
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21 <output name="snpeff_dbs">
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22 <assert_contents>
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23 <has_text text="ebola_zaire" />
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24 </assert_contents>
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25 </output>
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26 </test>
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27 </tests>
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28 <help><![CDATA[
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30 @EXTERNAL_DOCUMENTATION@
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32 ]]>
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33 </help>
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34 <expand macro="citations" />
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35 </tool>
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