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comparison scater-normalize.xml @ 0:0cb9a5f830fc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author iuc
date Thu, 18 Jul 2019 11:09:02 -0400
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-1:000000000000 0:0cb9a5f830fc
1 <tool id="scater_normalize" name="Scater: normalize SCE" version="@TOOL_VERSION@">
2 <description>Compute normalised expression values for SCE</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 Rscript '$__tool_directory__/scater-normalize.R'
9 -i '$input_loom'
10 -o '$output_loom'
11 ]]></command>
12 <inputs>
13 <param name="input_loom" type="data" format="loom" label="Input SingleCellLoomExperiment dataset to normalize" />
14 </inputs>
15 <outputs>
16 <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" />
17 </outputs>
18 <tests>
19 <test>
20 <param name="input_loom" value="scater_manual_filtered.loom" ftype="loom" />
21 <output name="output_loom" file="scater_filtered_normalised.loom" compare="sim_size" />
22 </test>
23 </tests>
24 <help><![CDATA[
25 Normalize a SingleCellLoomExperiment object using Scater. Adds 'logcounts' to assays slot.
26 ]]></help>
27 <expand macro="citations" />
28 </tool>