view dropletutils-read-10x.xml @ 6:ca62f52e0d7f draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit a1ad1ddd9b8e4db5bb82c3accae8311e0e488b19"

<?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}'

    #if $add_metadata.add_metadata_file 
    --metadata-files "${add_metadata.metadata_files}"
    --cell-id-column "${add_metadata.cell_id_column}" 
    #end if

]]></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"/>
    <conditional name="add_metadata">
        <param name="add_metadata_file" type="boolean" checked="false" label="Should metadata file be added?" />
        <when value="true" >
          <param name="metadata_files" type="data" label="Metadata file" help="Provide metadata file e.g. containing cell types"/>
          <param name="cell_id_column" type="text" label="Cell ID column" help="Cell ID column. Values must match those provided in the expression matrix." />
        </when>
      </conditional>
  </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="raw_sce.rds" ftype="rdata" compare="sim_size" delta="1000000"/>
    </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>