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

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author iuc
date Thu, 18 Jul 2019 11:11:45 -0400
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-1:000000000000 0:bea3359ba852
1 <tool id="scater_plot_pca" name="Scater: PCA plot" version="@TOOL_VERSION@">
2 <description>Plot cell-level reduced dimension of a normalised SCE</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$__tool_directory__/scater-plot-pca.R'
9 -i '$input_loom'
10 #if str($colour_by).strip():
11 --colour-by '$colour_by'
12 #end if
13 #if str($size_by).strip():
14 --size-by '$size_by'
15 #end if
16 #if str($shape_by).strip():
17 --shape-by '$shape_by'
18 #end if
19 -o '$output_plot'
20 ]]></command>
21 <inputs>
22 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
23 <param name="colour_by" argument="--colour-by" type="text" optional="true" label="Feature (from annotation file) to colour PCA plot points by" help="The values represented in this options should be categorical" />
24 <param name="size_by" argument="--size-by" type="text" optional="true" label="Feature (from annotation file) to size PCA plot points by" help="The values represented in this options should be numerical and not categorical" />
25 <param name="shape_by" argument="--shape-by" type="text" optional="true" label="Feature (from annotation file) to shape PCA plot points by" help="The values represented in this options should be categorical" />
26 </inputs>
27 <outputs>
28 <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
29 </outputs>
30 <tests>
31 <test>
32 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
33 <param name="colour_by" value="Treatment" />
34 <param name="shape_by" value="Mutation_Status" />
35 <output name="output_plot" file="scater_pca_plot.pdf" compare="sim_size" />
36 </test>
37 </tests>
38 <help><![CDATA[
39 Creates a PCA plot of a normalised SingleCellLoomExperiment object using Scater.
40 ]]></help>
41 <expand macro="citations" />
42 </tool>