annotate dropletutils-read-10x.xml @ 2:48c1e7b39675 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit 848d53f8dc662f24cc0443da6e5cacbd96daf5fe"

<?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>