Mercurial > repos > pjbriggs > trimmomatic

annotate trimmomatic_macros.xml @ 16:9a38087e3bfd draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
author iuc
date Sun, 14 Jan 2024 11:00:33 +0000
parents 32f1f56bd970
children b9aaed85cbd1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
1 <macros>
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
2 <!--
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
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).
pjbriggs
parents:
diff changeset
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).
pjbriggs
parents:
diff changeset
5 -->
14
d94aff5ee623 Version 0.38.1: add coreutils as dependency to fix tool issues with &#39;readlink -e&#39; across platforms.
pjbriggs
parents: 12
diff changeset
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
diff changeset
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>
15
32f1f56bd970 Updated for Trimmomatic 0.39 and adds quality score options.
pjbriggs
parents: 14
diff changeset
8 <token name="@TOOL_VERSION@">0.39</token>
16
9a38087e3bfd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/packages/trimmomatic commit ab36e4731731f12cce0e7d7cc3b50ba6a0bab1ef
iuc
parents: 15
diff changeset
9 <token name="@VERSION_SUFFIX@">1</token>
5
f80107cdc406 Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
pjbriggs
parents:
diff changeset
10 </macros>