diff scatter_plot_2D.xml @ 1:2e7d47c0b027 draft

"planemo upload for repository https://[e-mail]/repos/malex/secimtools"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scatter_plot_2D.xml	Mon Mar 08 22:04:06 2021 +0000
@@ -0,0 +1,154 @@
+<tool id="secimtools_scatter_plot_2D" name="Scatter Plot 2D" version="@WRAPPER_VERSION@">
+    <description>- A standalone tool.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+scatter_plot_2D.py
+--input $input
+--ID $uniqID
+
+--X $x
+--Y $y
+--figure $figure
+
+#if $design
+    --design $design
+#end if
+
+#if $group
+    --group $group
+#end if
+
+#if $color
+    --color $color
+#end if
+
+#if $palette
+    --palette $palette
+#end if
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="tabular" label="Long Dataset" help="Input dataset in tab-separated long format. Please see the description of the file format below. If the file is not tab separated see TIP below."/>
+        <param name="uniqID" type="text" size="30" value="" label="SampleID" help="Name of the column in your long dataset that has the unique sample idenifiers (sampleID)."/>
+        <param name="x" type="text" size="30" value="" label="X Group Title" help="Name of the column in your long format dataset for X values."/>
+        <param name="y" type="text" size="30" value="" label="Y Group Title" help="Name of the column in your long format dataset for Y values."/>
+        <param name="design" type="data" format="tabular" optional="true" label="Design File [Optional]" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
+        <param name="group" type="text" size="30" value="" label="Group/Treatment [Optional]" help="Name of the column in your design file that contains group classification to be used for coloring."/>
+        <param name="palette" type="text" size="30" label="Palette [Optional]" help="Select color palette. Default = tableau. Other options are diverging, qualitative, sequential, cubehelix, tableau, and  wesanderson. Please see the descriptions for the palettes below."/>
+        <param name="color" type="text" size="30" label="Color Scheme [Optional]" help="Select color scheme within the palette. Default color scheme for palette tableau = Tableau_20. User must specify a color scheme if the palette field has been filled. Please see the descriptions for the color schemes below."/>
+    </inputs>
+    <outputs>
+        <data format="pdf" name="figure" label="${tool.name} on ${on_string}: scatter plots"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input"   value="ST000006_principal_component_analysis_score_out.tsv"/>
+            <param name="design"  value="ST000006_design_group_name_underscore.tsv"/>
+            <param name="uniqID"  value="sampleID" />
+            <param name="group"   value="White_wine_type_and_source" />
+            <param name="x"       value="PC1" />
+            <param name="y"       value="PC2" />
+            <output name="figure" file="ST000006_scatter_plot_2D_default_figure.pdf" compare="sim_size" delta="10000"/>
+        </test>
+        <test>
+            <param name="input"   value="ST000006_principal_component_analysis_score_out.tsv"/>
+            <param name="design"  value="ST000006_design_group_name_underscore.tsv"/>
+            <param name="uniqID"  value="sampleID" />
+            <param name="group"   value="White_wine_type_and_source" />
+            <param name="x"       value="PC1" />
+            <param name="y"       value="PC2" />
+            <param name="palette" value="sequential" />
+            <param name="color"   value="Blues_3" />
+            <output name="figure" file="ST000006_scatter_plot_2D_palette_color_figure.pdf" compare="sim_size" delta="10000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@TIP_AND_WARNING@
+
+
+
+**Tool Description**
+
+The tool provides a 2D scatter plot of values in a Long Format file. Please see the description of the Long Format below.
+If coloring by group is desired, the column with the sample names in the Long Format dataset has to have the name "sampleID" to match the name in the Design File.
+Scatter plot 2D allows the user to plot any pair of values from the Principal Component Analysis (PCA) output or plot other data.
+
+NOTE: The user should ensure that the input datasets have no missing values.
+
+The user has an option to specify the palette and the color scheme within the palette.
+If the palette is specified by the user, the color scheme must to be specified.
+The list of available palettes are:
+
+diverging,
+qualitative,
+sequential,
+cubehelix,
+tableau (default), and
+wesanderson.
+
+The lists of corresponding color schemes for each palattes are available via the links below:
+
+
+https://jiffyclub.github.io/palettable/tableau/
+
+https://jiffyclub.github.io/palettable/colorbrewer/diverging/
+
+https://jiffyclub.github.io/palettable/colorbrewer/qualitative/
+
+https://jiffyclub.github.io/palettable/colorbrewer/sequential/
+
+https://jiffyclub.github.io/palettable/cubehelix/
+
+https://jiffyclub.github.io/palettable/wesanderson/
+
+
+--------------------------------------------------------------------------------
+
+**Input**
+
+    - Two input datasets are required.
+
+@LONG@
+
+
+**Sample ID**
+
+    - Name of the column in your Long Dataset that has unique sample IDs. If coloring by group, the sampleIDs must match the sampleIDs in the Design File (below).
+
+
+**X Group Title**
+
+    - Name of the column in the Long Format dataset for X values.
+
+**Y Group Title**
+
+    - Name of the column in the Long Format dataset for Y values.
+
+@DF@
+
+**Group/Treatment [Optional]**
+
+    - Name of the column in your Design File that contains group classification to be used for coloring.
+
+
+**Palette [Optional]**
+
+    - Choice of the palette. Default =  tableau. Other options include: diverging, qualitative, sequential, cubehelix, and wesanderson.
+
+**Color Scheme [Optional]**
+
+    - Choice of the color scheme within the palette. The default color scheme for palette tableau is Tableau_20. The user must specify the color scheme if the Palette field has been filled.
+
+--------------------------------------------------------------------------------
+
+**Output**
+
+The tool produces a PDF file with the 2D scatter plot.
+Coloring of the features by group and the corresponding legend will be included in the plot if the user provides a Design file and Palette.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>