diff scater-plot-dist-scatter.xml @ 1:2e41b35b5bdd draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 61f3899168453092fd25691cf31871a3a350fd3b"

--- a/scater-plot-dist-scatter.xml	Thu Jul 18 11:12:33 2019 -0400
+++ b/scater-plot-dist-scatter.xml	Tue Sep 03 14:25:32 2019 -0400
@@ -4,15 +4,18 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements">
-        <requirement type="package" version="0.2.1">r-ggpubr</requirement>
+        <requirement type="package" version="0.2.2">r-ggpubr</requirement>
+        <requirement type="package" version="1.0.0">r-scales</requirement>
     </expand>
     <command detect_errors="exit_code"><![CDATA[
 Rscript '$__tool_directory__/scater-plot-dist-scatter.R'
 -i '$input_loom'
 -o '$output_plot'
+$plot_log
     ]]></command>
     <inputs>
         <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset" />
+        <param name="plot_log" type="boolean" truevalue="--log-scale" falsevalue="" label="Plot on log scale" help="Recommended for large datasets" />
     </inputs>
     <outputs>
         <data name="output_plot" format="pdf" label="${tool.name} on ${on_string}" />
@@ -20,8 +23,14 @@
     <tests>
         <test>
             <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
+            <param name="plot_log" value="false"/>
             <output name="output_plot" file="scater_reads_genes_dist.pdf" compare="sim_size" />
         </test>
+        <test>
+            <param name="input_loom" value="scater_qcready.loom" ftype="loom" />
+            <param name="plot_log" value="true"/>
+            <output name="output_plot" file="scater_reads_genes_dist_log.pdf" compare="sim_size" />
+        </test>
     </tests>
     <help><![CDATA[
 Plot distribution of reads and features for single-cell RNA-seq analysis using Scater.