comparison dropletutils-read-10x.xml @ 5:3dd08eb96cf6 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit ed7141cff329d11308fe2556eeb01d51bfaa6759"

4:d552332dff6d

<?xml version="1.0" encoding="utf-8"?>
<tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy1">
  <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)"/>

5:3dd08eb96cf6

<?xml version="1.0" encoding="utf-8"?>
<tool id="dropletutils_read_10x" name="DropletUtils Read10x" version="@TOOL_VERSION@+galaxy2">
  <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)"/>