Mercurial > repos > iuc > snpeff

annotate snpEff_databases.xml @ 8:1501e66908de draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
author iuc
date Fri, 16 Sep 2016 13:06:31 -0400
parents aaa749ea91a2
children 81fba81425a4
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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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11 @CONDA_SNPEFF_JAR_PATH@ &&
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12 java -jar "\$SNPEFF_JAR_PATH/snpEff.jar" databases | grep -v '^---' | sed 's/^Genome/#Genome/' | sed 's/ *//g' > "$snpeff_dbs"
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13 ]]>
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14 </command>
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15 <inputs>
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16 </inputs>
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17 <outputs>
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18 <data format="tabular" name="snpeff_dbs" label="${tool.name} @SNPEFF_VERSION@ available databases" />
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19 </outputs>
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20 <tests>
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21 <test>
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22 <output name="snpeff_dbs">
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23 <assert_contents>
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24 <has_text text="ebola_zaire" />
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25 </assert_contents>
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26 </output>
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27 </test>
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28 </tests>
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29 <help><![CDATA[
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31 @EXTERNAL_DOCUMENTATION@
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33 ]]>
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34 </help>
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35 <expand macro="citations" />
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36 </tool>
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