Mercurial > repos > richard-burhans > ncbi_egapx
changeset 36:304fe17cd5b3 draft
planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 913ef1a671c8002fd57e1b25b80f6b2ebc9ae6bd
| author | richard-burhans |
|---|---|
| date | Wed, 18 Jun 2025 19:45:34 +0000 |
| parents | ff65a73f5379 |
| children | bd764dc23da1 |
| files | macros.xml ncbi_egapx.xml |
| diffstat | 2 files changed, 3 insertions(+), 4 deletions(-) [+] |
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--- a/macros.xml Tue Apr 01 15:11:11 2025 +0000 +++ b/macros.xml Wed Jun 18 19:45:34 2025 +0000 @@ -5,7 +5,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">0.3.2-alpha</token> - <token name="@VERSION_SUFFIX@">8</token> + <token name="@VERSION_SUFFIX@">9</token> <token name="@PROFILE@">23.0</token> <xml name="edam_ontology"> <edam_operations>
--- a/ncbi_egapx.xml Tue Apr 01 15:11:11 2025 +0000 +++ b/ncbi_egapx.xml Wed Jun 18 19:45:34 2025 +0000 @@ -51,8 +51,7 @@ ## - nextflow conda environment ## - EGPAx python virtual environment source /galaxy/env.bash && - ## use the augmented container EGAPx config - ln -s /galaxy/egapx/egapx_config && + python3 /galaxy/scripts/galaxy-resource-config.py && ## run EGAPx python3 /galaxy/egapx/ui/egapx.py '$yamlconfig' -e galaxy -o 'egapx_out' && ## hack to support 0.2-alpha @@ -211,7 +210,7 @@ <data name="run_timeline" format="html" label="Nextflow execution timeline" from_work_dir="egapx_out/run.timeline.html"/> <data name="nextflow_log" format="txt" label="Nextflow execution log" from_work_dir="egapx_out/nextflow.log"/> <data name="run_trace" format="tabular" label="Nextflow trace file" from_work_dir="egapx_out/run.trace.txt"/> - <data name="run_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/> + <data name="run_params" format="yaml" label="Nextflow run parameters" from_work_dir="egapx_out/run_params.yaml"/> </collection> <collection name="star_alignments" type="list" label="EGAPx STAR alignments for ${on_string}"> <discover_datasets pattern="(?:.+/)?bam\.[0-9A-Za-z]{10}/(?P<designation>.+)\.bam" format="bam" directory="egapx_out" recurse="true" match_relative_path="true"/>