| Next changeset 1:2e81fbe036b2 (2019-10-22) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 67729956c77554abbaf1d4fd0edf19215eff28da-dirty |
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matrix-service.xml |
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| diff -r 000000000000 -r c127d4124583 matrix-service.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matrix-service.xml Tue Jul 02 11:10:16 2019 -0400 |
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| @@ -0,0 +1,108 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="hca_matrix_downloader" name="Human Cell Atlas Matrix Downloader" version="v0.0.2+galaxy0"> + <description>retrieves expression matrices and metadata from the Human Cell Atlas.</description> + <requirements> + <requirement type="package" version="0.0.2">hca-matrix-downloader</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + +hca-matrix-downloader -p '${project}' -f mtx -o out -f '${matrix_format}' + +#if $matrix_format == "mtx": + && hca-mtx-to-10x out.mtx . + && gunzip -c out.mtx/cells.tsv.gz > exp_design.tsv +#end if + +]]></command> + + <inputs> + <param name="project" type="text" value="Single cell transcriptome analysis of human pancreas" label="Human Cell Atlas project name/label/UUID" help="HCA project identifier, can be project title, project label or project UUID."/> + <param name="matrix_format" type="select" label="Choose the format of matrix to download" help="Matrix Market or Loom"> + <option value="mtx" selected="true">Matrix Market</option> + <option value="loom">Loom</option> + </param> + </inputs> + + <outputs> + <data name="matrix_mtx" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string} matrix.mtx"> + <filter>matrix_format=="mtx"</filter> + </data> + <data name="genes_tsv" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string} genes.tsv"> + <filter>matrix_format=="mtx"</filter> + </data> + <data name="barcode_tsv" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string} barcodes.tsv"> + <filter>matrix_format=="mtx"</filter> + </data> + <data name="cells_meta_tsv" format="tsv" from_work_dir="exp_design.tsv" label="${tool.name} on ${on_string} exp_design.tsv"> + <filter>matrix_format=="mtx"</filter> + </data> + <data name="matrix_loom" format="h5" from_work_dir="out.loom" label="${tool.name} on ${on_string} matrix.loom"> + <filter>matrix_format=="loom"</filter> + </data> + </outputs> + + <tests> + <test> + <param name="project" value="Single cell transcriptome analysis of human pancreas"/> + <param name="matrix_format" value="mtx"/> + <output name="matrix_mtx" file="matrix.mtx" ftype="txt"/> + <output name="genes_tsv" file="genes.tsv" ftype="tsv"/> + <output name="barcode_tsv" file="barcodes.tsv" ftype="tsv"/> + <output name="cells_meta_tsv" file="exp_design.tsv" ftype="tsv"/> + </test> + </tests> + + <help><![CDATA[ +=========================================================================== +Down expression matrix from HCA projects using HCA DCP's matrix service API +=========================================================================== + +The data retrieval tool presented here allows the user to retrieve expression matrices +and metadata for any public experiment available at Human Cell Atlas data portal. + +To use it, simply set the name, or label, or ID for the desired project, which can be +found at the HCA data browser (https://prod.data.humancellatlas.org/explore/projects), +and select the desired matrix format (Matrix Market or Loom). + +Outputs will be: + +- *When "Matrix Market" is seleted, outputs are in 10X-compatible Matrix Market format:* + + 1. **Matrix (txt):** + + Contains the expression values for genes (rows) and cells (columns) in raw counts. This + text file is formatted as a Matrix Market file, and as such it is accompanied by separate + files for the gene identifiers and the cells identifiers. + + 2. **Genes (tsv):** + + Identifiers (column repeated) for the genes present in the matrix of expression, + in the same order as the matrix rows. + + 3. **Barcodes (tsv):** + + Identifiers for the cells of the data matrix. The file is ordered to match the columns + of the matrix. + + 4. **Experiment Design file (tsv):** + + Contains metadata for the different cells of the experiment. + +- *When "Loom" is selected, output is a single Loom HDF5 file:* + + 1. **Loom (h5):** + + Contains expression values for genes (rows) and cells (columns) in raw counts, cell + metadata table and gene metadata table, in a single HDF5 file with specification defined + in http://linnarssonlab.org/loompy/format/index.html. + +**Version history** + + 0.0.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Teichmann Lab at Wellcome Sanger Institute and + Expression Atlas team https://www.ebi.ac.uk/gxa/home at EMBL-EBI https://www.ebi.ac.uk/. + +]]></help> + <citations> + <citation type="doi">10.7554/eLife.27041</citation> + </citations> +</tool> |