Mercurial > repos > iuc > scater_create_qcmetric_ready_sce
comparison 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 |
|---|---|
| date | Thu, 18 Jul 2019 11:14:06 -0400 |
| parents | |
| children | b834074a9aff |
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| -1:000000000000 | 0:2d455a7e8a3d |
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| 1 <tool id="scater_create_qcmetric_ready_sce" name="Scater: Calculate QC metrics" version="@TOOL_VERSION@"> | |
| 2 <description>Computes QC metrics from single-cell expression matrix</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <command detect_errors="exit_code"><![CDATA[ | |
| 8 Rscript '$__tool_directory__/scater-create-qcmetric-ready-sce.R' | |
| 9 -a '$counts' | |
| 10 #if $col_data: | |
| 11 -c '$col_data' | |
| 12 #end if | |
| 13 #if $mt_controls: | |
| 14 -f '$mt_controls' | |
| 15 #end if | |
| 16 #if $ercc_controls: | |
| 17 -p '$ercc_controls' | |
| 18 #end if | |
| 19 #if $cell_controls: | |
| 20 -l '$cell_controls' | |
| 21 #end if | |
| 22 -o '$output_loom' | |
| 23 ]]></command> | |
| 24 <inputs> | |
| 25 <param name="counts" type="data" format="tabular" label="Expression matrix in tabular format" help="The first column of all files is assumed to be feature names and the first row is assumed to be sample names" /> | |
| 26 <param name="col_data" type="data" format="tabular" optional="true" label="Format dataset describing the features in tabular format" help="The number of rows (samples) must equal the number of columns in the expression matrix" /> | |
| 27 <param name="mt_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the mitochondrial control genes" /> | |
| 28 <param name="ercc_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the ERCC controls" /> | |
| 29 <param name="cell_controls" type="data" format="txt" optional="true" label="Dataset containing the list of the cell controls" help="Cell (sample) names used to identify cell controls (for example, blank wells or bulk controls)" /> | |
| 30 </inputs> | |
| 31 <outputs> | |
| 32 <data name="output_loom" format="loom" label="${tool.name} on ${on_string}" /> | |
| 33 </outputs> | |
| 34 <tests> | |
| 35 <test> | |
| 36 <param name="counts" value="counts.txt" /> | |
| 37 <param name="col_data" value="annotation.txt" /> | |
| 38 <param name="mt_controls" value="mt_controls.txt" /> | |
| 39 <output name="output_loom" file="scater_qcready.loom" compare="sim_size" /> | |
| 40 </test> | |
| 41 </tests> | |
| 42 <help><![CDATA[ | |
| 43 Calculate QC metrics for single-cell RNA-seq analysis using Scater. | |
| 44 ]]></help> | |
| 45 <expand macro="citations" /> | |
| 46 </tool> |