comparison scanpy_macros2.xml @ 25:6b97ffba31da draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 6c9d530aa653101e9e21804393ec11f38cddf027-dirty

24:439f7f939d46

<macros>
  <token name="@TOOL_VERSION@">1.8.1+3</token>
  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
  <token name="@PROFILE@">18.01</token>
  <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**

1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper.

1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc.

      <option value="loom">Loom format hdf5</option>
    </param>
  </xml>

  <xml name="output_object_params">
    <param name="output_format" argument="--output-format" type="select" label="Format of output object">
      <option value="anndata_h5ad" selected="true">AnnData format</option>
      <option value="anndata">AnnData format (h5 for older versions)</option>
      <option value="loom">Loom format</option>
      <option value="loom_legacy">Loom format (h5 for older versions)</option>
    </param>
  </xml>

  <xml name="output_object_params_no_loom">
    <param name="output_format" argument="--output-format" type="select" label="Format of output object">
      <option value="anndata_h5ad" selected="true">AnnData format</option>
      <option value="anndata">AnnData format (h5 for older versions)</option>
    </param>
  </xml>

  <xml name="output_data_obj_no_loom" token_description="operation">
    <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
      <filter>output_format == 'anndata_h5ad'</filter>
    </data>
    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
      <filter>output_format == 'anndata'</filter>
    </data>
  </xml>

  <xml name="output_data_obj" token_description="operation">
    <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
      <filter>output_format == 'anndata_h5ad'</filter>
    </data>
    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
      <filter>output_format == 'anndata'</filter>
    </data>
    <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
      <filter>output_format == 'loom_legacy'</filter>
    </data>
    <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
      <filter>output_format == 'loom'</filter>
    </data>
  </xml>

  <xml name="save_matrix_params">

25:6b97ffba31da

<macros>
  <token name="@TOOL_VERSION@">1.8.1</token>
  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
  <token name="@PROFILE@">18.01</token>
  <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**
1.8.1+galaxy9: Fixes version label to get versions sorted properly on Galaxy (equivalent to 1.8.1+3+galaxy0). In addition, adds ability to make fields unique in AnnData operations,
adds additional handler on Scrubblet for workflows convenience, enables Scanpy tools to avoid outputing AnnData/matrix files when not required.

1.8.1+3+galaxy0: Upate to scanpy-scripts 1.1.3 (running scanpy ==1.8.1), including a fix to MTX output and a bugfix for the Scrublet wrapper.

1.8.1+2+galaxy0: Upate to scanpy-scripts 1.1.2 (running scanpy ==1.8.1), including improved boolean handling for mito etc.

      <option value="loom">Loom format hdf5</option>
    </param>
  </xml>

  <xml name="output_object_params">
    <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="AnnData or Loom. Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
      <option value="anndata_h5ad" selected="true">AnnData format</option>
      <option value="anndata">AnnData format (h5 for older versions)</option>
      <option value="loom">Loom format</option>
      <option value="loom_legacy">Loom format (h5 for older versions)</option>
      <option value="no_matrix_output">No packaged matrix output</option>
    </param>
  </xml>

  <xml name="output_object_params_no_loom">
    <param name="output_format" argument="--output-format" type="select" label="Format of output object" help="Legacy 'h5' datatypes are useful for interacting with older tools. Choosing 'No packaged matrix output' is useful for cases where auxiliary files are generated (like in marker genes). Do not use when there are no other output files, as the tool will generate no output in Galaxy then.">
      <option value="anndata_h5ad" selected="true">AnnData format</option>
      <option value="anndata">AnnData format (h5 for older versions)</option>
      <option value="no_matrix_output">No packaged matrix output (useful for cases where auxiliary files are generated)</option>
    </param>
  </xml>

  <xml name="output_data_obj_no_loom" token_description="operation">
    <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
      <filter>output_format == 'anndata_h5ad'</filter>
    </data>
    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
      <filter>output_format == 'anndata'</filter>
    </data>
  </xml>

  <xml name="output_data_obj" token_description="operation">
    <data name="output_h5ad" format="h5ad" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData">
      <filter>output_format == 'anndata_h5ad'</filter>
    </data>
    <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ AnnData (h5)">
      <filter>output_format == 'anndata'</filter>
    </data>
    <data name="output_loom_legacy" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom">
      <filter>output_format == 'loom_legacy'</filter>
    </data>
    <data name="output_loom" format="loom" from_work_dir="output.h5" label="${tool.name} on ${on_string}: @DESCRIPTION@ Loom (h5)">
      <filter>output_format == 'loom'</filter>
    </data>
  </xml>

  <xml name="save_matrix_params">