Mercurial > repos > iuc > scater_plot_dist_scatter

diff scater-plot-dist-scatter.xml @ 0:ff695f98c32c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author: iuc
date: Thu, 18 Jul 2019 11:08:33 -0400
children: 86c3ee9d9f49
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scater-plot-dist-scatter.xml	Thu Jul 18 11:08:33 2019 -0400
@@ -0,0 +1,30 @@
+<tool id="scater_plot_dist_scatter" name="Scater: plot library QC" version="@TOOL_VERSION@">
+    <description>Create plots to visualise library size, feature counts and mito gene expression</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="0.2.1">r-ggpubr</requirement>
+    </expand>
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/scater-plot-dist-scatter.R'
+-i '$input_loom'
+-o '$output_plot'
+    ]]></command>
+    <inputs>
+        <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
+    </inputs>
+    <outputs>
+        <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
+            <output name="output_plot" file="scater_reads_genes_dist.pdf" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Plot distribution of reads and features for single-cell RNA-seq analysis using Scater.
+    ]]></help>
+    <expand macro="citations" />
+</tool>