Mercurial > repos > iuc > scater_create_qcmetric_ready_sce
diff scater-create-qcmetric-ready-sce.xml @ 0:2d455a7e8a3d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scater commit 5fdcafccb6c645d301db040dfeed693d7b6b4278
author | iuc |
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date | Thu, 18 Jul 2019 11:14:06 -0400 |
parents | |
children | b834074a9aff |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scater-create-qcmetric-ready-sce.xml Thu Jul 18 11:14:06 2019 -0400 @@ -0,0 +1,46 @@ +<tool id="scater_create_qcmetric_ready_sce" name="Scater: Calculate QC metrics" version="@TOOL_VERSION@"> + <description>Computes QC metrics from single-cell expression matrix</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ +Rscript '$__tool_directory__/scater-create-qcmetric-ready-sce.R' +-a '$counts' +#if $col_data: + -c '$col_data' +#end if +#if $mt_controls: + -f '$mt_controls' +#end if +#if $ercc_controls: + -p '$ercc_controls' +#end if +#if $cell_controls: + -l '$cell_controls' +#end if +-o '$output_loom' + ]]></command> + <inputs> + <param name="counts" type="data" format="tabular" label="Expression matrix in tabular format" help="The first column of all files is assumed to be feature names and the first row is assumed to be sample names" /> + <param name="col_data" type="data" format="tabular" optional="true" label="Format dataset describing the features in tabular format" help="The number of rows (samples) must equal the number of columns in the expression matrix" /> + <param name="mt_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the mitochondrial control genes" /> + <param name="ercc_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the ERCC controls" /> + <param name="cell_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the cell controls" help="Cell (sample) names used to identify cell controls (for example, blank wells or bulk controls)" /> + </inputs> + <outputs> + <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="counts" value="counts.txt" /> + <param name="col_data" value="annotation.txt" /> + <param name="mt_controls" value="mt_controls.txt" /> + <output name="output_loom" file="scater_qcready.loom" compare="sim_size" /> + </test> + </tests> + <help><![CDATA[ +Calculate QC metrics for single-cell RNA-seq analysis using Scater. + ]]></help> + <expand macro="citations" /> +</tool>