Mercurial > repos > iuc > scater_plot_pca
annotate scater-plot-pca.xml @ 3:c99ba278dfa9 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 9961b5acbf9081f10e14bc272406b36854fa2924"
author | iuc |
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date | Mon, 08 Nov 2021 12:01:49 +0000 |
parents | 9e5c0bb18d08 |
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9e5c0bb18d08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
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1 <tool id="scater_plot_pca" name="Scater: PCA plot" version="@TOOL_VERSION@" profile="@PROFILE@"> |
9e5c0bb18d08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
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2 <description>cell-level reduced dimension of a normalised SCE</description> |
9e5c0bb18d08
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 154318f74839a4481c7c68993c4fb745842c4cce"
iuc
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3 <expand macro="bio_tools"/> |
0
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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4 <macros> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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5 <import>macros.xml</import> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
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changeset
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6 </macros> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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7 <expand macro="requirements" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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8 <command detect_errors="exit_code"><![CDATA[ |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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9 Rscript '$__tool_directory__/scater-plot-pca.R' |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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10 -i '$input_loom' |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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11 #if str($colour_by).strip(): |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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12 --colour-by '$colour_by' |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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13 #end if |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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14 #if str($size_by).strip(): |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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15 --size-by '$size_by' |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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16 #end if |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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17 #if str($shape_by).strip(): |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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18 --shape-by '$shape_by' |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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19 #end if |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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20 -o '$output_plot' |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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21 ]]></command> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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22 <inputs> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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23 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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24 <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" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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25 <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" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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26 <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" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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27 </inputs> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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28 <outputs> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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29 <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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30 </outputs> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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31 <tests> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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32 <test> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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33 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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34 <param name="colour_by" value="Treatment" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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35 <param name="shape_by" value="Mutation_Status" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
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36 <output name="output_plot" file="scater_pca_plot.pdf" compare="sim_size" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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37 </test> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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38 </tests> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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39 <help><![CDATA[ |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
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40 Creates a PCA plot of a normalised SingleCellLoomExperiment object using Scater. |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
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41 ]]></help> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
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42 <expand macro="citations" /> |
bea3359ba852
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
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43 </tool> |