# HG changeset patch # User q2d2 # Date 1661802419 0 # Node ID dda27bfef1413a1a7ed0bbc2c6c0cfc2bb103577 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 diff -r 000000000000 -r dda27bfef141 qiime2__diversity_lib__unweighted_unifrac.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__diversity_lib__unweighted_unifrac.xml Mon Aug 29 19:46:59 2022 +0000 @@ -0,0 +1,237 @@ + + + + + Unweighted Unifrac + + quay.io/qiime2/core:2022.8 + + q2galaxy version diversity_lib + q2galaxy run diversity_lib unweighted_unifrac '$inputs' + + + + + + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]'] + + + + + + hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]'] + +
+ + + + + + + + + + + + + +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +QIIME 2: diversity-lib unweighted-unifrac +========================================= +Unweighted Unifrac + + +Outputs: +-------- +:distance_matrix.qza: Distance matrix for Unweighted Unifrac. + +| + +Description: +------------ +Compute Unweighted Unifrac for each sample in a feature table + +Examples: +--------- + +run on one core (by default) +**************************** +Using the ``qiime2 diversity-lib unweighted-unifrac`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Set *"phylogeny"* to ``#: phylogeny.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 unweighted-unifrac [...] : distance_matrix.qza`` + - ``unweighted-unifrac-dm.qza`` + +to run on n cores, replace 1 here with your preferred integer +************************************************************* +Using the ``qiime2 diversity-lib unweighted-unifrac`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Set *"phylogeny"* to ``#: phylogeny.qza`` + #. Expand the ``additional options`` section + + - Leave *"threads"* 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 unweighted-unifrac [...] : distance_matrix.qza`` + - ``unweighted-unifrac-dm.qza`` + +use 'auto' to run on all of host system's available CPU cores +************************************************************* +Using the ``qiime2 diversity-lib unweighted-unifrac`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Set *"phylogeny"* to ``#: phylogeny.qza`` + #. Expand the ``additional options`` section + + - Set *"threads"* 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 unweighted-unifrac [...] : distance_matrix.qza`` + - ``unweighted-unifrac-dm.qza`` + +use bypass_tips to trade specificity for reduced compute time +************************************************************* +| bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time. +Using the ``qiime2 diversity-lib unweighted-unifrac`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Set *"phylogeny"* to ``#: phylogeny.qza`` + #. Expand the ``additional options`` section + + #. Set *"threads"* to ``auto`` + #. Set *"bypass_tips"* to ``Yes`` + + #. 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 unweighted-unifrac [...] : distance_matrix.qza`` + - ``unweighted-unifrac-dm.qza`` + + +| + + + + 10.1128/AEM.71.12.8228-8235.2005 + 10.1128/AEM.01996-06 + 10.1038/ismej.2009.97 + 10.1038/ismej.2010.133 + 10.1038/s41592-018-0187-8 + 10.1038/s41587-019-0209-9 + +
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