| Next changeset 1:f25f42dc256a (2019-11-11) |
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Commit message:
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 9bf9a6e46a330890be932f60d1d996dd166426c4 |
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added:
dropletutils-read-10x.xml dropletutils_macros.xml |
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| diff -r 000000000000 -r d62a9aa0411e dropletutils-read-10x.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dropletutils-read-10x.xml Wed Apr 03 11:59:13 2019 -0400 |
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| @@ -0,0 +1,57 @@ +<?xml version="1.0" encoding="utf-8"?> +<tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy0"> + <description>into SingleCellExperiment object</description> + <macros> + <import>dropletutils_macros.xml</import> + </macros> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +ln -s '${matrix}' matrix.mtx && +ln -s '${genes}' genes.tsv && +ln -s '${barcodes}' barcodes.tsv && +dropletutils-read-10x-counts.R + -s . + -c TRUE + -o '${output_rds}' +]]></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"/> + </inputs> + + <outputs> + <data name="output_rds" format="rdata" label="${tool.name} on ${on_string}: serialized SingleCellExperiment object"/> + </outputs> + + <tests> + <test> + <param name="matrix" value="matrix.mtx"/> + <param name="genes" value="genes.tsv"/> + <param name="barcodes" value="barcodes.tsv"/> + <output name="output_rds" file="read_10x.rds" ftype="rdata" compare="sim_size"/> + </test> + </tests> + + <help><![CDATA[ +============================================================= +Read 10x-Genomics-formatted mtx directory (`Read10xCounts()`) +============================================================= + +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. + + +@HELP@ +]]></help> + <expand macro="citations"/> +</tool> |
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| diff -r 000000000000 -r d62a9aa0411e dropletutils_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dropletutils_macros.xml Wed Apr 03 11:59:13 2019 -0400 |
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| @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<macros> + + <token name="@TOOL_VERSION@">1.0.3</token> + + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.0.1">dropletutils-scripts</requirement> + </requirements> + </xml> + + <xml name="version"> + <version_command><![CDATA[ + echo $(R --version | grep version | grep -v GNU)", dropletutils version" $(R --vanilla --slave -e "library(DropletUtils); cat(sessionInfo()\$otherPkgs\$DropletUtils\$Version)" 2> /dev/null | grep -v -i "WARNING: ") + ]]></version_command> + </xml> + + <xml name="citations"> + <citations> + <citation type="doi">10.1101/234872</citation> + </citations> + </xml> +</macros> |