Mercurial > repos > iuc > snpeff

annotate snpEff_macros.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 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="4.1">snpEff</requirement>
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5 </requirements>
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6 </xml>
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7 <xml name="stdio">
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8 <stdio>
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9 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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10 <exit_code range="1:" level="fatal" description="Error" />
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11 </stdio>
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12 </xml>
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1501e66908de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
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13 <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
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14 <xml name="version_command">
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15 <version_command><![CDATA[
1501e66908de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
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16 if [ -z "$SNPEFF_JAR_PATH" ]; then
1501e66908de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
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17 export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
1501e66908de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
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18 fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
1501e66908de planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 00efb7078cfb3664ef048925d0a6b02d8578c27d
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19 ]]></version_command>
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20 </xml>
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21 <token name="@WRAPPER_VERSION@">4.1</token>
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22 <token name="@SNPEFF_VERSION@">SnpEff4.1</token>
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23 <token name="@SNPEFF_DATABASE_URL@">https://snpeff-data.galaxyproject.org/databases/v4_1/</token>
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24 <token name="@EXTERNAL_DOCUMENTATION@">
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26 For details about this tool, please go to:
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27 http://snpeff.sourceforge.net/SnpEff_manual.html
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29 </token>
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30 <xml name="citations">
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31 <citations>
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32 <citation type="doi">10.4161/fly.19695</citation>
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33 <yield />
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34 </citations>
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35 </xml>
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36 </macros>