# HG changeset patch # User q2d2 # Date 1661802471 0 # Node ID 1eca9b532c76e9251cb4b399d79a86f13afac0f4 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 diff -r 000000000000 -r 1eca9b532c76 qiime2__diversity_lib__jaccard.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__diversity_lib__jaccard.xml Mon Aug 29 19:47:51 2022 +0000 @@ -0,0 +1,187 @@ + + + + + Jaccard Distance + + quay.io/qiime2/core:2022.8 + + q2galaxy version diversity_lib + q2galaxy run diversity_lib jaccard '$inputs' + + + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] + +
+ + + + + + + + + + + + +
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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +QIIME 2: diversity-lib jaccard +============================== +Jaccard Distance + + +Outputs: +-------- +:distance_matrix.qza: Distance matrix for Jaccard index + +| + +Description: +------------ +Compute Jaccard distance for each sample in a feature table. Jaccard is calculated usingpresence/absence data. Data of type FeatureTable[Frequency | Relative Frequency] is reducedto presence/absence prior to calculation. + +Examples: +--------- + +run on one core (by default) +**************************** +Using the ``qiime2 diversity-lib jaccard`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`` + - ``jaccard-dm.qza`` + +to run on n cores, replace 1 here with your preferred integer +************************************************************* +Using the ``qiime2 diversity-lib jaccard`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Expand the ``additional options`` section + + - Leave *"n_jobs"* as its default value of ``1`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`` + - ``jaccard-dm.qza`` + +use 'auto' to run on all of host system's available CPU cores +************************************************************* +Using the ``qiime2 diversity-lib jaccard`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Expand the ``additional options`` section + + - Set *"n_jobs"* to ``auto`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 diversity-lib jaccard [...] : distance_matrix.qza`` + - ``jaccard-dm.qza`` + + +| + + + + @article{cite1, + author = {Jaccard, P}, + journal = {Bull. Soc. Vard. Sci. Nat}, + pages = {223--270}, + title = {Nouvelles recherches sur la distribution floral}, + volume = {44}, + year = {1908} +} + + 10.1038/s41587-019-0209-9 + +
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