Mercurial > repos > pjbriggs > trimmomatic
comparison trimmomatic_macros.xml @ 15:32f1f56bd970 draft
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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| 14:d94aff5ee623 | 15:32f1f56bd970 |
|---|---|
| 3 Set the path for the trimmomatic JAR and data files | 3 Set the path for the trimmomatic JAR and data files |
| 4 Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13 | 4 Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13 |
| 5 --> | 5 --> |
| 6 <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi</token> | 6 <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi</token> |
| 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> | 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> |
| 8 <token name="@TOOL_VERSION@">0.39</token> | |
| 9 <token name="@VERSION_SUFFIX@">0</token> | |
| 8 </macros> | 10 </macros> |