From f0617bf7ae8d8d5bb6f3caa5f76f50e0f971a198 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 6 Oct 2022 23:29:01 +0200 Subject: [PATCH 1/2] add qiime qzv visualisation extractor the qiime2 display application (view.qiime2.org) does not work for non-public Galaxy instances. This is a workaround. qiime2 viz artifacts are just zip files which also contain the html + data + files (which is shown at the view website). So this tool is equivalent If I find the time I will explore the possibility to do the same with a generic / viz plugin .. at least for so long (and maybe for workflows) the tool will be useful. --- tools/qiime_extract_viz/.shed.yml | 10 +++ tools/qiime_extract_viz/qiime_extract_viz.xml | 78 ++++++++++++++++++ .../test-data/demux-summ.qzv | Bin 0 -> 318218 bytes tools/qiime_extract_viz/test-data/qiime2.qzv | Bin 0 -> 6686 bytes 4 files changed, 88 insertions(+) create mode 100644 tools/qiime_extract_viz/.shed.yml create mode 100644 tools/qiime_extract_viz/qiime_extract_viz.xml create mode 100644 tools/qiime_extract_viz/test-data/demux-summ.qzv create mode 100644 tools/qiime_extract_viz/test-data/qiime2.qzv diff --git a/tools/qiime_extract_viz/.shed.yml b/tools/qiime_extract_viz/.shed.yml new file mode 100644 index 00000000000..bf81a57ab45 --- /dev/null +++ b/tools/qiime_extract_viz/.shed.yml @@ -0,0 +1,10 @@ +name: qiime_extract_viz +owner: iuc +description: Extract vizualization from QIIME artifacts +long_description: | + TODO +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz +homepage_url: http://www.qiime.org +type: unrestricted +categories: + - Metagenomics diff --git a/tools/qiime_extract_viz/qiime_extract_viz.xml b/tools/qiime_extract_viz/qiime_extract_viz.xml new file mode 100644 index 00000000000..e90fc53cbc0 --- /dev/null +++ b/tools/qiime_extract_viz/qiime_extract_viz.xml @@ -0,0 +1,78 @@ + + + + 0.1.0 + 0 + + + topic_3174 + + + operation_2422 + + + unzip + + + ## Galaxy sets application/octet-stream as mime type for which browsers + ## refuse to include the file. Therefore we replace the extensions by js + ## for which Galaxy sets the appropriate mime type + for nonjs in \$(cat '${viz.extra_files_path}'/*.html | grep '