Mercurial > repos > iuc > scater_plot_dist_scatter
annotate scater-plot-dist-scatter.xml @ 1:2e41b35b5bdd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
author | iuc |
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date | Tue, 03 Sep 2019 14:25:32 -0400 |
parents | 4887c4c69847 |
children | 81e5bdff4853 |
rev | line source |
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4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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1 <tool id="scater_plot_dist_scatter" name="Scater: plot library QC" version="@TOOL_VERSION@"> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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2 <description>Create plots to visualise library size, feature counts and mito gene expression</description> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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3 <macros> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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4 <import>macros.xml</import> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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5 </macros> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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6 <expand macro="requirements"> |
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2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
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7 <requirement type="package" version="0.2.2">r-ggpubr</requirement> |
2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
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8 <requirement type="package" version="1.0.0">r-scales</requirement> |
0
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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9 </expand> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
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10 <command detect_errors="exit_code"><![CDATA[ |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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11 Rscript '$__tool_directory__/scater-plot-dist-scatter.R' |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
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12 -i '$input_loom' |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
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13 -o '$output_plot' |
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2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
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14 $plot_log |
0
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
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15 ]]></command> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
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16 <inputs> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
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17 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" /> |
1
2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
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18 <param name="plot_log" type="boolean" truevalue="--log-scale" falsevalue="" label="Plot on log scale" help="Recommended for large datasets" /> |
0
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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19 </inputs> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
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20 <outputs> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
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21 <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" /> |
4887c4c69847
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 </outputs> |
4887c4c69847
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 <tests> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
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24 <test> |
4887c4c69847
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="input_loom" value="scater_qcready.loom" ftype="loom" /> |
1
2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
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26 <param name="plot_log" value="false"/> |
0
4887c4c69847
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 <output name="output_plot" file="scater_reads_genes_dist.pdf" compare="sim_size" /> |
4887c4c69847
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 </test> |
1
2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
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29 <test> |
2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
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30 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> |
2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
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31 <param name="plot_log" value="true"/> |
2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
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32 <output name="output_plot" file="scater_reads_genes_dist_log.pdf" compare="sim_size" /> |
2e41b35b5bdd
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"
iuc
parents:
0
diff
changeset
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33 </test> |
0
4887c4c69847
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 </tests> |
4887c4c69847
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 <help><![CDATA[ |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
changeset
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36 Plot distribution of reads and features for single-cell RNA-seq analysis using Scater. |
4887c4c69847
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 ]]></help> |
4887c4c69847
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 <expand macro="citations" /> |
4887c4c69847
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
iuc
parents:
diff
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39 </tool> |