comparison scanpy-read-10x.xml @ 5:f180f7230cdb draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003

4:741d50b6dc78

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy0">
  <description>into hdf5 object handled by scanpy</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    <param name="cell_meta" type="data" format="tsv,tabular" label="Cell metadata table" optional="true"
           help="Requires a header row and index column that matches the barcode/cell table"/>
    <param name="gene_meta" type="data" format="tsv,tabular" label="Gene metadata table" optional="true"
           help="Requires a header row and index column that matches the gene table"/>
    <expand macro="output_object_params"/>
    <param name="var_names" type="select" label="Attribute used as annotation index">
      <option value="gene_ids" selected="true">Gene ID</option>
      <option value="gene_symbols">Gene symbol</option>
    </param>
  </inputs>

  <outputs>
    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: ${output_format}"/>
  </outputs>

  <tests>
    <test>
      <param name="matrix" value="matrix.mtx"/>

5:f180f7230cdb

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_read_10x" name="Scanpy Read10x" version="@TOOL_VERSION@+galaxy6">
  <description>into hdf5 object handled by scanpy</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    <param name="cell_meta" type="data" format="tsv,tabular" label="Cell metadata table" optional="true"
           help="Requires a header row and index column that matches the barcode/cell table"/>
    <param name="gene_meta" type="data" format="tsv,tabular" label="Gene metadata table" optional="true"
           help="Requires a header row and index column that matches the gene table"/>
    <expand macro="output_object_params"/>
    <param name="var_names" type="select" label="Attribute used as annotation index" help="If Gene ID is selected the index will point to the gene identifiers (first columns expected) and the gene symbols will be left in a field called 'gene_symbols'.">
      <option value="gene_ids" selected="true">Gene ID</option>
      <option value="gene_symbols">Gene symbol</option>
    </param>
  </inputs>

  <outputs>
    <expand macro="output_data_obj" description="${output_format}"/>
  </outputs>

  <tests>
    <test>
      <param name="matrix" value="matrix.mtx"/>