Mercurial > repos > iuc > scater_plot_tsne

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 9961b5acbf9081f10e14bc272406b36854fa2924"
author iuc
date Mon, 08 Nov 2021 12:00:14 +0000
parents 244263a3193e
children
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244263a3193e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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1 <tool id="scater_plot_tsne" name="Scater: t-SNE plot" version="@TOOL_VERSION@" profile="@PROFILE@">
244263a3193e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
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2 <description>of two components</description>
1
821d1ab87d8f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools"/>
0
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4 <macros>
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5 <import>macros.xml</import>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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6 </macros>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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7 <expand macro="requirements">
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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8 <requirement type="package" version="0.15">r-rtsne</requirement>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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9 </expand>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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10 <command detect_errors="exit_code"><![CDATA[
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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11 Rscript '$__tool_directory__/scater-plot-tsne.R'
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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12 -i '$input_loom'
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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13 #if str($colour_by).strip():
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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14 --colour-by '$colour_by'
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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15 #end if
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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16 #if str($size_by).strip():
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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17 --size-by '$size_by'
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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18 #end if
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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19 #if str($shape_by).strip():
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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20 --shape-by '$shape_by'
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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21 #end if
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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22 -o '$output_plot'
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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23 ]]></command>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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24 <inputs>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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25 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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26 <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" />
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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27 <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" />
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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28 <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" />
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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29 </inputs>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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30 <outputs>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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31 <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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32 </outputs>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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33 <tests>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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34 <test>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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35 <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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36 <param name="colour_by" value="Treatment" />
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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37 <param name="shape_by" value="Mutation_Status" />
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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38 <output name="output_plot" file="scater_tsne_plot.pdf" compare="sim_size" />
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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39 </test>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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40 </tests>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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41 <help><![CDATA[
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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42 Creates a t-SNE plot of a normalised SingleCellLoomExperiment object using Scater.
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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43 ]]></help>
e5e00c1c975a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
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44 <expand macro="citations" />
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45 </tool>