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annotate trimmomatic_macros.xml @ 15:32f1f56bd970 draft

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Updated for Trimmomatic 0.39 and adds quality score options.
author pjbriggs
date Thu, 02 Mar 2023 15:24:24 +0000
parents d94aff5ee623
children 9a38087e3bfd
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f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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1 <macros>
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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2 <!--
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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3 Set the path for the trimmomatic JAR and data files
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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4 Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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5 -->
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d94aff5ee623 Version 0.38.1: add coreutils as dependency to fix tool issues with &#39;readlink -e&#39; across platforms.
pjbriggs
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6 <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi</token>
d94aff5ee623 Version 0.38.1: add coreutils as dependency to fix tool issues with &#39;readlink -e&#39; across platforms.
pjbriggs
parents: 12
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7 <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi</token>
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32f1f56bd970 Updated for Trimmomatic 0.39 and adds quality score options.
pjbriggs
parents: 14
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8 <token name="@TOOL_VERSION@">0.39</token>
32f1f56bd970 Updated for Trimmomatic 0.39 and adds quality score options.
pjbriggs
parents: 14
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9 <token name="@VERSION_SUFFIX@">0</token>
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f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
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10 </macros>