comparison dropletutils-read-10x.xml @ 3:058a41379291 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit e1ed5cbba4d1c042b91cefec41f98e7c736dfbe2"

2:48c1e7b39675

<?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"/>

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>

3:058a41379291

<?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"/>

ln -s '${barcodes}' barcodes.tsv &&
dropletutils-read-10x-counts.R
    -s .
    -c TRUE
    -o '${output_rds}'

#if $add_metadata_file 
--metadata-files "${metadata_files}" 
--cell-id-column "${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>