Mercurial > repos > iuc > scater_plot_tsne

comparison scater-plot-tsne.xml @ 0:e5e00c1c975a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author iuc
date Tue, 03 Sep 2019 14:24:21 -0400
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-1:000000000000 0:e5e00c1c975a
1 <tool id="scater_plot_tsne" name="Scater: t-SNE plot" version="@TOOL_VERSION@">
2 <description>Produces a t-SNE plot of two components</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements">
7 <requirement type="package" version="0.15">r-rtsne</requirement>
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[
10 Rscript '$__tool_directory__/scater-plot-tsne.R'
11 -i '$input_loom'
12 #if str($colour_by).strip():
13 --colour-by '$colour_by'
14 #end if
15 #if str($size_by).strip():
16 --size-by '$size_by'
17 #end if
18 #if str($shape_by).strip():
19 --shape-by '$shape_by'
20 #end if
21 -o '$output_plot'
22 ]]></command>
23 <inputs>
24 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
25 <param name="colour_by" argument="--colour-by" type="text" optional="true" label="Feature (from annotation file) to colour t-SNE plot points by" help="The values represented in this options should be categorical" />
26 <param name="size_by" argument="--size-by" type="text" optional="true" label="Feature (from annotation file) to size t-SNE plot points by" help="The values represented in this options should be numerical and not categorical" />
27 <param name="shape_by" argument="--shape-by" type="text" optional="true" label="Feature (from annotation file) to shape t-SNE plot points by" help="The values represented in this options should be categorical" />
28 </inputs>
29 <outputs>
30 <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
31 </outputs>
32 <tests>
33 <test>
34 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
35 <param name="colour_by" value="Treatment" />
36 <param name="shape_by" value="Mutation_Status" />
37 <output name="output_plot" file="scater_tsne_plot.pdf" compare="sim_size" />
38 </test>
39 </tests>
40 <help><![CDATA[
41 Creates a t-SNE plot of a normalised SingleCellLoomExperiment object using Scater.
42 ]]></help>
43 <expand macro="citations" />
44 </tool>