Mercurial > repos > iuc > snpsift

annotate snpSift_macros.xml @ 14:80da7fae14b8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:10:54 -0500
parents ed810da439cc
children 8bd645802765
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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4 <requirement type="package" version="4.1">snpsift</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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80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
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13 <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token>
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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14 <xml name="version_command">
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80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
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15 <version_command><![CDATA[
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
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16 if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
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17 java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
80da7fae14b8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
iuc
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18 ]]></version_command>
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ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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19 </xml>
ed810da439cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit d12a2e9dd273b4c23db48bbb747f32700887710e
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20 <token name="@WRAPPER_VERSION@">4.1</token>
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21 <token name="@EXTERNAL_DOCUMENTATION@">
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23 For details about this tool, please go to:
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24 http://snpeff.sourceforge.net/SnpEff_manual.html
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25
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26 </token>
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27 <xml name="citations">
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28 <citations>
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29 <citation type="doi">10.3389/fgene.2012.00035</citation>
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30 <yield />
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31 </citations>
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32 </xml>
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33 </macros>