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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit d13a0a5fceabe51e1a6fe763767b963623aa295a
author | ebi-gxa |
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date | Mon, 28 Oct 2019 05:26:50 -0400 |
parents | 3faf577f3e40 |
children | f180f7230cdb |
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<?xml version="1.0" encoding="utf-8"?> <tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0"> <description>into hdf5 object handled by scanpy</description> <macros> <import>scanpy_macros2.xml</import> </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ ln -s '${matrix}' matrix.mtx && ln -s '${genes}' genes.tsv && ln -s '${barcodes}' barcodes.tsv && PYTHONIOENCODING=utf-8 scanpy-read-10x --input-10x-mtx ./ --var-names '${var_names}' #if $cell_meta: --extra-obs '${cell_meta}' #end if #if $gene_meta: --extra-var '${gene_meta}' #end if @OUTPUT_OPTS@ ]]></command> <inputs> <param name="matrix" type="data" format="txt" label="Expression matrix in sparse matrix format (.mtx)"/> <param name="genes" type="data" format="tsv,tabular" label="Gene table"/> <param name="barcodes" type="data" format="tsv,tabular" label="Barcode/cell table"/> <param name="cell_meta" type="data" format="tsv,tabular" label="Cell metadata table" optional="true" help="Requires a header row and index column that matches the barcode/cell table"/> <param name="gene_meta" type="data" format="tsv,tabular" label="Gene metadata table" optional="true" help="Requires a header row and index column that matches the gene table"/> <expand macro="output_object_params"/> <param name="var_names" type="select" label="Attribute used as annotation index"> <option value="gene_ids" selected="true">Gene ID</option> <option value="gene_symbols">Gene symbol</option> </param> </inputs> <outputs> <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: ${output_format}"/> </outputs> <tests> <test> <param name="matrix" value="matrix.mtx"/> <param name="genes" value="genes.tsv"/> <param name="barcodes" value="barcodes.tsv"/> <!-- <param name="cell_meta" value=""/> --> <param name="output_format" value="anndata"/> <output name="output_h5" file="output.h5" ftype="h5" compare="sim_size"/> </test> </tests> <help><![CDATA[ ================================================================= Read 10x-Genomics-formatted mtx directory (`scanpy.read_10x_mtx`) ================================================================= The mtx directory should contain: 1) Raw expression quantification as a sparse matrix in Matrix Market format, where the each column is a gene and each row is a barcode/cell. 2) A gene table of at least two columns where the first column gives the gene IDs. 3) A barcode/cell table of at least one column giving the barcode/cell IDs. The above-mentioned files can be obtained by running `EBI SCXA Data Retrieval` with a dataset accession or `Human Cell Atlas Matrix Downloader` with a project name/label/UUID. Additionally, cell and/or gene metadata table can be provided as tab-separated text with a header row and an index column that matches the respective barcode/cell and/or gene table. @HELP@ @VERSION_HISTORY@ ]]></help> <expand macro="citations"/> </tool>