# HG changeset patch # User q2d2 # Date 1730318374 0 # Node ID df9f1ff48c2934102d734335b6552258f9f1d0dd planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard commit 5f71b597c9495eae67a447744fded834f56ca1f7 diff -r 000000000000 -r df9f1ff48c29 qiime2__vizard__lineplot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__vizard__lineplot.xml Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,396 @@ + + + + + Lineplot + + qiime2 + + + quay.io/qiime2/amplicon:2024.10 + + q2galaxy version vizard + q2galaxy run vizard lineplot '$inputs' + + + + + + + + + + + + + + + + + + + + + + + value is not None and len(value) > 0 + + + + + + value is not None and len(value) > 0 + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +QIIME 2: vizard lineplot +======================== +Lineplot + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Basic lineplot for visualizing two numeric Metadata measures with optional grouping. All numeric columns present in the Metadata will be available as drop-down options on the Y-axis, but the chosen `x_measure` remains fixed. + +Examples: +--------- + +lineplot_median_replicates_with_grouping +**************************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``median`` + #. Set *"group_by"* to ``group`` + #. Set *"title"* to ``Lineplot with median replicate method, grouped by `group`.`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_mean_replicates_with_grouping +************************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``mean`` + #. Set *"group_by"* to ``group`` + #. Set *"title"* to ``Lineplot with mean replicate method, grouped by `group`.`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_median_replicates_no_grouping +************************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``median`` + #. Set *"title"* to ``Lineplot with median replicate method (no grouping).`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_mean_replicates_no_grouping +************************************ +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``x`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"replicate_method"* to ``mean`` + #. Set *"title"* to ``Lineplot with mean replicate method (no grouping).`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_no_replicates_with_grouping +************************************ +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``a`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + #. Set *"group_by"* to ``group`` + #. Set *"title"* to ``Lineplot with no replicate method, grouped by `group`.`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + +lineplot_no_replicates_no_grouping +********************************** +Using the ``qiime2 vizard lineplot`` tool: + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"x_measure"* to ``b`` + #. Set *"y_measure"* to ``y`` + #. Expand the ``additional options`` section + + - Set *"title"* to ``Lineplot with no replicate method (no grouping).`` + + #. 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 vizard lineplot [...] : visualization.qzv`` + - ``lineplot.qzv`` + + +| + + + + 10.1038/s41587-019-0209-9 + +
diff -r 000000000000 -r df9f1ff48c29 test-data/heatmap.test0.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/heatmap.test0.metadata.tsv Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff -r 000000000000 -r df9f1ff48c29 test-data/lineplot.test0.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test0.metadata.tsv Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff -r 000000000000 -r df9f1ff48c29 test-data/lineplot.test1.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test1.metadata.tsv Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff -r 000000000000 -r df9f1ff48c29 test-data/lineplot.test2.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test2.metadata.tsv Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff -r 000000000000 -r df9f1ff48c29 test-data/lineplot.test3.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test3.metadata.tsv Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff -r 000000000000 -r df9f1ff48c29 test-data/lineplot.test4.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test4.metadata.tsv Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff -r 000000000000 -r df9f1ff48c29 test-data/lineplot.test5.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/lineplot.test5.metadata.tsv Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff -r 000000000000 -r df9f1ff48c29 test-data/scatterplot_2d.test0.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scatterplot_2d.test0.metadata.tsv Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 4 6 1 1 +sample02 aa 5 9 2 2 +sample03 aa 3 1 3 3 +sample04 aa 5 3 4 5 +sample05 aa 5 7 5 8 +sample06 bb 2 4 1 10 +sample07 bb 3 9 2 15 +sample08 bb 3 3 3 20 +sample09 bb 5 5 4 22 +sample10 bb 4 3 5 27 +sample11 bb 3 7 6 33 +sample12 bb 5 5 7 36 +sample13 bb 2 9 8 39 +sample14 cc 4 7 1 40 +sample15 cc 2 2 2 41 +sample16 cc 4 4 3 43 +sample17 cc 5 9 4 47 +sample18 cc 1 2 5 50 +sample19 cc 4 9 6 60 diff -r 000000000000 -r df9f1ff48c29 test-data/scatterplot_2d.test1.metadata.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scatterplot_2d.test1.metadata.tsv Wed Oct 30 19:59:34 2024 +0000 @@ -0,0 +1,21 @@ +sample_name group x y a b +#q2:types categorical numeric numeric numeric numeric +sample01 aa 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