Mercurial > repos > iuc > scater_normalize

diff scater-normalize.xml @ 0:87757f7b9974 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author: iuc
date: Thu, 18 Jul 2019 11:13:05 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scater-normalize.xml	Thu Jul 18 11:13:05 2019 -0400
@@ -0,0 +1,28 @@
+<tool id="scater_normalize" name="Scater: normalize SCE" version="@TOOL_VERSION@">
+    <description>Compute normalised expression values for SCE</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+Rscript '$__tool_directory__/scater-normalize.R'
+-i '$input_loom'
+-o '$output_loom'
+    ]]></command>
+    <inputs>
+        <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset to normalize" />
+    </inputs>
+    <outputs>
+        <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_loom" value="scater_manual_filtered.loom" ftype="loom" />
+            <output name="output_loom" file="scater_filtered_normalised.loom" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Normalize a SingleCellLoomExperiment object using Scater. Adds 'logcounts' to assays slot.
+    ]]></help>
+    <expand macro="citations" />
+</tool>