Mercurial > repos > ebi-gxa > seurat_normalise_data
diff seurat_normalise_data.xml @ 1:48174ec556de draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 0463f230d18201c740851d72e31a5024f391207f
author | ebi-gxa |
---|---|
date | Mon, 25 Nov 2019 06:13:04 -0500 |
parents | 619fead82856 |
children | 9d92ec597603 |
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--- a/seurat_normalise_data.xml Wed Apr 03 11:20:42 2019 -0400 +++ b/seurat_normalise_data.xml Mon Nov 25 06:13:04 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="seurat_normalise_data" name="Seurat NormaliseData" version="2.3.1+galaxy1"> +<tool id="seurat_normalise_data" name="Seurat NormaliseData" version="@SEURAT_VERSION@_@VERSION@+galaxy0"> <description>normalise data</description> <macros> <import>seurat_macros.xml</import> @@ -8,7 +8,7 @@ <command detect_errors="exit_code"><![CDATA[ seurat-normalise-data.R ---input-object-file '$input' +@INPUT_OBJECT@ #if $norm: --normalization-method $norm #end if @@ -18,12 +18,17 @@ #if $scale: --scale-factor $scale #end if ---output-object-file '$output' +@OUTPUT_OBJECT@ ]]></command> <inputs> - <param name="input" argument="--input-object-file" type="data" format="rdata" label="Seurat RDS object" help="Possibly the output of Seurat filter cells or Seurat create object." /> - <param name="norm" argument="--normalization-method" type="text" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize)."/> + <expand macro="input_object_params"/> + <expand macro="output_object_params"/> + <param name="norm" argument="--normalization-method" type="select" optional="True" label="Normalisation method" help = "Method for normalization. Default is log-normalization (LogNormalize). Can be 'CLR' or 'RC' additionally."> + <option value="LogNormalize" selected="true">Log Normalise</option> + <option value="CLR">CLR</option> + <option value="RC">RC</option> + </param> <param name="assay" argument="--assay-type" type="text" optional="True" label="Assay type" help = "Type of assay to normalize for (default is RNA), but can be changed for multimodal analyses."> <validator type="regex" message="Please only use letters">^[\(\w\)]+$</validator> </param> @@ -31,13 +36,13 @@ </inputs> <outputs> - <data name="output" format="rdata" from_work_dir="*.rds" label="${tool.name} on ${on_string}: RDS file"/> + <expand macro="output_files"/> </outputs> <tests> <test> <param name="input" ftype="rdata" value="seurat.rds"/> - <output name="output" ftype="rdata" value="out_norm.rds" compare="sim_size"/> + <output name="rds_seurat_file" ftype="rdata" value="out_norm.rds" compare="sim_size"/> </test> </tests> <help><![CDATA[ @@ -45,12 +50,9 @@ **What it does** -Seurat_ is a toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. -It is developed and maintained by the `Satija Lab`_ at NYGC. Seurat aims to enable users to identify and -interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse -types of single cell data. +This tool normalises a Seurat RDS object. -This tool normalises a Seurat RDS object. +@SEURAT_INTRO@ -----