Mercurial > repos > iuc > scater_plot_dist_scatter
comparison 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 |
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0:4887c4c69847 | 1:2e41b35b5bdd |
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2 <description>Create plots to visualise library size, feature counts and mito gene expression</description> | 2 <description>Create plots to visualise library size, feature counts and mito gene expression</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"> | 6 <expand macro="requirements"> |
7 <requirement type="package" version="0.2.1">r-ggpubr</requirement> | 7 <requirement type="package" version="0.2.2">r-ggpubr</requirement> |
8 <requirement type="package" version="1.0.0">r-scales</requirement> | |
8 </expand> | 9 </expand> |
9 <command detect_errors="exit_code"><![CDATA[ | 10 <command detect_errors="exit_code"><![CDATA[ |
10 Rscript '$__tool_directory__/scater-plot-dist-scatter.R' | 11 Rscript '$__tool_directory__/scater-plot-dist-scatter.R' |
11 -i '$input_loom' | 12 -i '$input_loom' |
12 -o '$output_plot' | 13 -o '$output_plot' |
14 $plot_log | |
13 ]]></command> | 15 ]]></command> |
14 <inputs> | 16 <inputs> |
15 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" /> | 17 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" /> |
18 <param name="plot_log" type="boolean" truevalue="--log-scale" falsevalue="" label="Plot on log scale" help="Recommended for large datasets" /> | |
16 </inputs> | 19 </inputs> |
17 <outputs> | 20 <outputs> |
18 <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" /> | 21 <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" /> |
19 </outputs> | 22 </outputs> |
20 <tests> | 23 <tests> |
21 <test> | 24 <test> |
22 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> | 25 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> |
26 <param name="plot_log" value="false"/> | |
23 <output name="output_plot" file="scater_reads_genes_dist.pdf" compare="sim_size" /> | 27 <output name="output_plot" file="scater_reads_genes_dist.pdf" compare="sim_size" /> |
28 </test> | |
29 <test> | |
30 <param name="input_loom" value="scater_qcready.loom" ftype="loom" /> | |
31 <param name="plot_log" value="true"/> | |
32 <output name="output_plot" file="scater_reads_genes_dist_log.pdf" compare="sim_size" /> | |
24 </test> | 33 </test> |
25 </tests> | 34 </tests> |
26 <help><![CDATA[ | 35 <help><![CDATA[ |
27 Plot distribution of reads and features for single-cell RNA-seq analysis using Scater. | 36 Plot distribution of reads and features for single-cell RNA-seq analysis using Scater. |
28 ]]></help> | 37 ]]></help> |