Galaxy |

Changeset 0:df9f1ff48c29 (2024-10-30)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vizard commit 5f71b597c9495eae67a447744fded834f56ca1f7

added:
qiime2__vizard__lineplot.xml
test-data/heatmap.test0.metadata.tsv
test-data/lineplot.test0.metadata.tsv
test-data/lineplot.test1.metadata.tsv
test-data/lineplot.test2.metadata.tsv
test-data/lineplot.test3.metadata.tsv
test-data/lineplot.test4.metadata.tsv
test-data/lineplot.test5.metadata.tsv
test-data/scatterplot_2d.test0.metadata.tsv
test-data/scatterplot_2d.test1.metadata.tsv

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

[

b'@@ -0,0 +1,396 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<tool name="qiime2 vizard lineplot" id="qiime2__vizard__lineplot" version="0.0.1.dev0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">\n+ <description>Lineplot</description>\n+ <xrefs>\n+ <xref type="bio.tools">qiime2</xref>\n+ </xrefs>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/amplicon:2024.10</container>\n+ </requirements>\n+ <version_command>q2galaxy version vizard</version_command>\n+ <command detect_errors="exit_code">q2galaxy run vizard lineplot \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="staging_path_and_source_path"/>\n+ </configfiles>\n+ <inputs>\n+ <repeat name="metadata" min="1" help="[required] Any metadata-like input with at least two numeric measures for visualizing." title="metadata: Metadata">\n+ <conditional name="__q2galaxy__GUI__conditional__metadata__">\n+ <param name="type" type="select" label="metadata: Metadata">\n+ <option value="tsv" selected="true">Metadata from TSV</option>\n+ <option value="qza">Metadata from Artifact</option>\n+ </param>\n+ <when value="tsv">\n+ <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>\n+ </when>\n+ <when value="qza">\n+ <param name="source" type="data" format="qza" label="Metadata Source"/>\n+ </when>\n+ </conditional>\n+ </repeat>\n+ <param name="x_measure" type="text" label="x_measure: Str" help="[required] Numeric measure from the input Metadata that should be plotted on the x-axis.">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ <param name="y_measure" type="text" label="y_measure: Str" help="[required] Numeric measure from the input Metadata that should be plotted on the y-axis.">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <param name="replicate_method" type="select" label="replicate_method: Str % Choices(\'none\', \'median\', \'mean\')" display="radio">\n+ <option value="none" selected="true">none</option>\n+ <option value="median">median</option>\n+ <option value="mean">mean</option>\n+ </param>\n+ <conditional name="__q2galaxy__GUI__conditional__group_by__" label="group_by: Str">\n+ <param name="__q2galaxy__GUI__select__" type="select" label="group_by: Str" help="[optional] Categorical measure from the input Metadata that should be used for grouping the lineplot.">\n+ <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>\n+ <option value="__q2galaxy__::control::provide">Provide a value</option>\n+ </param>\n+ <when value="__q2galaxy__::control::default">\n+ <param name="group_by" type="hidden" value="__q2galaxy__::literal::None"/>\n+ </when>\n+ <when value="__q2galaxy__::control::provide">\n+ <param name="group_by" type="text">\n+ '..b'plot.qzv``\n+\n+lineplot_median_replicates_no_grouping\n+**************************************\n+Using the ``qiime2 vizard lineplot`` tool:\n+ #. For *"metadata"*:\n+\n+ - Perform the following steps.\n+\n+ #. Leave as ``Metadata from TSV``\n+ #. Set *"Metadata Source"* to ``metadata.tsv``\n+\n+\n+ #. Set *"x_measure"* to ``x``\n+ #. Set *"y_measure"* to ``y``\n+ #. Expand the ``additional options`` section\n+\n+ #. Set *"replicate_method"* to ``median``\n+ #. Set *"title"* to ``Lineplot with median replicate method (no grouping).``\n+\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``\n+ - ``lineplot.qzv``\n+\n+lineplot_mean_replicates_no_grouping\n+************************************\n+Using the ``qiime2 vizard lineplot`` tool:\n+ #. For *"metadata"*:\n+\n+ - Perform the following steps.\n+\n+ #. Leave as ``Metadata from TSV``\n+ #. Set *"Metadata Source"* to ``metadata.tsv``\n+\n+\n+ #. Set *"x_measure"* to ``x``\n+ #. Set *"y_measure"* to ``y``\n+ #. Expand the ``additional options`` section\n+\n+ #. Set *"replicate_method"* to ``mean``\n+ #. Set *"title"* to ``Lineplot with mean replicate method (no grouping).``\n+\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``\n+ - ``lineplot.qzv``\n+\n+lineplot_no_replicates_with_grouping\n+************************************\n+Using the ``qiime2 vizard lineplot`` tool:\n+ #. For *"metadata"*:\n+\n+ - Perform the following steps.\n+\n+ #. Leave as ``Metadata from TSV``\n+ #. Set *"Metadata Source"* to ``metadata.tsv``\n+\n+\n+ #. Set *"x_measure"* to ``a``\n+ #. Set *"y_measure"* to ``y``\n+ #. Expand the ``additional options`` section\n+\n+ #. Set *"group_by"* to ``group``\n+ #. Set *"title"* to ``Lineplot with no replicate method, grouped by `group`.``\n+\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``\n+ - ``lineplot.qzv``\n+\n+lineplot_no_replicates_no_grouping\n+**********************************\n+Using the ``qiime2 vizard lineplot`` tool:\n+ #. For *"metadata"*:\n+\n+ - Perform the following steps.\n+\n+ #. Leave as ``Metadata from TSV``\n+ #. Set *"Metadata Source"* to ``metadata.tsv``\n+\n+\n+ #. Set *"x_measure"* to ``b``\n+ #. Set *"y_measure"* to ``y``\n+ #. Expand the ``additional options`` section\n+\n+ - Set *"title"* to ``Lineplot with no replicate method (no grouping).``\n+\n+ #. Press the ``Execute`` button.\n+\n+Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows:\n+ (Renaming is optional, but it will make any subsequent steps easier to complete.)\n+\n+ .. list-table::\n+ :align: left\n+ :header-rows: 1\n+\n+ * - History Name\n+ - *"Name"* to set (be sure to press ``Save``)\n+ * - ``#: qiime2 vizard lineplot [...] : visualization.qzv``\n+ - ``lineplot.qzv``\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'

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

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

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

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

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

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

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

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