Mercurial > repos > iuc > qiime_extract_viz
changeset 0:f1605d46cb42 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiimme_extract_viz commit 19abce82000b612039fa835391a6fb9328368d73
| author | iuc |
|---|---|
| date | Mon, 13 May 2024 09:25:59 +0000 |
| parents | |
| children | |
| files | qiime_extract_viz.xml test-data/demux-summ.qzv test-data/qiime2.qzv |
| diffstat | 3 files changed, 78 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime_extract_viz.xml Mon May 13 09:25:59 2024 +0000 @@ -0,0 +1,78 @@ +<tool id="qiime_extract_viz" name="QIIME vizualisation extractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.01" license="MIT"> + <description></description> + <macros> + <token name="@TOOL_VERSION@">0.1.0</token> + <token name="@VERSION_SUFFIX@">0</token> + </macros> + <edam_topics> + <edam_topic>topic_3174</edam_topic><!-- metagenomics --> + </edam_topics> + <edam_operations> + <edam_operation>operation_2422</edam_operation> <!-- Data retrieval --> + </edam_operations> + <requirements> + <requirement type="package" version="6.0">unzip</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + unzip '$infile' "*/data/*" && + mkdir -p '${viz.extra_files_path}' && + mv '$infile.metadata.uuid'/data/* '${viz.extra_files_path}' && + + ## the html file use <script src="./data.jsonp" charset="utf-8"></script> + ## 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 '${viz.extra_files_path}'/*.html | grep '<script src="' | sed 's/^\s*<script src="//; s/".*//' | grep -v "\.js\$"); do + js=\$(echo "\$nonjs" | sed 's/\.[^.]\+$//').js && + mv '${viz.extra_files_path}'"/\$nonjs" '${viz.extra_files_path}'"/\$js" && + sed -i -e "s@\"\${nonjs}\"@\"\${js}\"@" '${viz.extra_files_path}'/*.html; + done && + + mv '${viz.extra_files_path}'/index.html '$viz' + ]]></command> + <inputs> + <param name="infile" type="data" format="qzv" label="QIIME visualization artifact" /> + </inputs> + <outputs> + <data name="viz" format="html"/> + </outputs> + <tests> + <!-- the first test use the test data from the galaxy datatypes module + where the html file just contains 43 --> + <test> + <param name="infile" value="qiime2.qzv" ftype="qzv"/> + <output name="viz"> + <assert_contents> + <has_text text="43"/> + </assert_contents> + </output> + </test> + <test> + <param name="infile" value="demux-summ.qzv" ftype="qzv"/> + <output name="viz"> + <assert_contents> + <has_text text="html"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +The tool extracts visualisation from QIIME visualisation artifact datasets (qzv). + +QIIME visualisation artifact files are zip files that contain visualisations of the data +which is extracted by this tool. + +Note that Galaxy contains a Display application that uses +https://view.qiime2.org/ to show this data. For non-public Galaxy instances this +does not work. + + ]]></help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool> \ No newline at end of file