diff scater-plot-pca.xml @ 0:bea3359ba852 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scater-plot-pca.xml	Thu Jul 18 11:11:45 2019 -0400
@@ -0,0 +1,42 @@
+<tool id="scater_plot_pca" name="Scater: PCA plot" version="@TOOL_VERSION@">
+    <description>Plot cell-level reduced dimension of a normalised SCE</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/scater-plot-pca.R'
+-i '$input_loom'
+#if str($colour_by).strip():
+    --colour-by '$colour_by'
+#end if
+#if str($size_by).strip():
+    --size-by '$size_by'
+#end if
+#if str($shape_by).strip():
+    --shape-by '$shape_by'
+#end if
+-o '$output_plot'
+    ]]></command>
+    <inputs>
+        <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
+        <param name="colour_by" argument="--colour-by" type="text" optional="true" label="Feature (from annotation file) to colour PCA plot points by" help="The values represented in this options should be categorical" />
+        <param name="size_by" argument="--size-by" type="text" optional="true" label="Feature (from annotation file) to size PCA plot points by" help="The values represented in this options should be numerical and not categorical" />
+        <param name="shape_by" argument="--shape-by" type="text" optional="true" label="Feature (from annotation file) to shape PCA plot points by" help="The values represented in this options should be categorical" />
+    </inputs>
+    <outputs>
+        <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
+            <param name="colour_by" value="Treatment" />
+            <param name="shape_by" value="Mutation_Status" />
+            <output name="output_plot" file="scater_pca_plot.pdf" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Creates a PCA plot of a normalised SingleCellLoomExperiment object using Scater.
+    ]]></help>
+    <expand macro="citations" />
+</tool>