Mercurial > repos > iuc > scater_plot_dist_scatter

comparison scater-plot-dist-scatter.xml @ 1:86c3ee9d9f49 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 14:21:22 -0400
parents ff695f98c32c
children dcda8e123809
comparison
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0:ff695f98c32c 1:86c3ee9d9f49
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>