Mercurial > repos > artbio > gsc_scran_normalize
diff scran_normalize.xml @ 2:6864acb21714 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/gsc_scran_normalize commit a14fb3d106b647c4f1dea2c8d3ac7c1e8848b21c
author | artbio |
---|---|
date | Sun, 10 Dec 2023 00:27:45 +0000 |
parents | fb2f1b8b0013 |
children |
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--- a/scran_normalize.xml Sun Dec 04 01:01:01 2022 +0000 +++ b/scran_normalize.xml Sun Dec 10 00:27:45 2023 +0000 @@ -1,8 +1,9 @@ -<tool id="scran_normalize" name="scran_normalize" version="0.2.1"> +<tool id="scran_normalize" name="scran_normalize" version="1.28.1+galaxy0"> <description>Normalize raw counts expression values using deconvolution size factors</description> <requirements> - <requirement type="package" version="1.6.2">r-optparse</requirement> - <requirement type="package" version="1.12.1=r36he1b5a44_0">bioconductor-scran</requirement> + <requirement type="package" version="1.28.1">bioconductor-scran</requirement> + <requirement type="package" version="1.63_1">r-dynamictreecut</requirement> + <requirement type="package" version="1.7.3">r-optparse</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> @@ -10,7 +11,6 @@ <command detect_errors="exit_code"><![CDATA[ Rscript $__tool_directory__/scran-normalize.R --data '$input' - --sep '$input_sep' #if $metacell.cluster == "Yes": --cluster --method '$metacell.method' @@ -19,11 +19,7 @@ -o '${output}' ]]></command> <inputs> - <param name="input" type="data" format="txt,tabular" label="Raw counts of expression data" help = "Must have an header"/> - <param name="input_sep" type="select" label="Input column separator"> - <option value="tab" selected="true">Tabulation</option> - <option value=",">Comma</option> - </param> + <param name="input" type="data" format="tabular" label="Raw counts of expression data" help = "A tsv file that must have an header line"/> <conditional name="metacell"> <param name="cluster" type="select" label = "Do you want to cluster cells ?" help="Perform scaling method on metacell, see Details"> <option value="Yes">Yes</option> @@ -45,18 +41,18 @@ </outputs> <tests> <test> - <param name="input" value="counts.tab" ftype="tabular"/> - <output name="output" file="logcounts.tab" ftype="tabular"/> + <param name="input" value="counts.tsv" ftype="tabular"/> + <output name="output" file="logcounts.tsv" ftype="tabular"/> </test> <test> - <param name="input" value="counts.tab" ftype="tabular"/> + <param name="input" value="counts.tsv" ftype="tabular"/> <param name="cluster" value="Yes"/> <param name="method" value="igraph"/> <param name="size" value="25"/> <output name="output" file="logcounts_igraph.tsv" ftype="tabular"/> </test> <test> - <param name="input" value="counts.tab" ftype="tabular"/> + <param name="input" value="counts.tsv" ftype="tabular"/> <param name="cluster" value="Yes"/> <param name="method" value="hclust"/> <param name="size" value="25"/>