comparison scanpy_macros2.xml @ 4:47603f46d6d9 draft

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

3:8e45c89adab2

<macros>
  <token name="@TOOL_VERSION@">1.4.3</token>
  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
  <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**

1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).

1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).

    ]]></token>
  <token name="@INPUT_OPTS@">
    --input-format '${input_format}' input.h5
  </token>
  <token name="@OUTPUT_OPTS@">
    --show-obj stdout --output-format '${output_format}' output.h5
  </token>
  <token name="@PLOT_OPTS@">
#if $fig_title
    --title '${fig_title}'
#end if

  </token>
  <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="0.2.6">scanpy-scripts</requirement>
      <yield/>
    </requirements>
  </xml>

  <xml name="citations">

      }</citation>
    </citations>
  </xml>

  <xml name="input_object_params">
    <param name="input_obj_file" argument="input-object-file" type="data" format="h5" label="Input object in hdf5 format"/>
    <param name="input_format" argument="--input-format" type="select" label="Format of input object">
      <option value="anndata" selected="true">AnnData format hdf5</option>
      <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" selected="true">AnnData format hdf5</option>
      <option value="loom">Loom format hdf5</option>
    </param>
  </xml>

  <xml name="output_plot_params">
    <param name="fig_title" argument="--title" type="text" label="Figure title"/>
    <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>

4:47603f46d6d9

<macros>
  <token name="@TOOL_VERSION@">1.4.3</token>
  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
  <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**

1.4.3+galaxy6: Update to scanpy-scripts 0.2.8 (running scanpy ==1.4.3) and wider compatibility with other Galaxy modules. Bug fixes in filtering and plotting improvements.

1.4.3+galaxy0: Update to scanpy-scripts 0.2.5 (running scanpy ==1.4.3).

1.4.2+galaxy0: Update to scanpy-scripts 0.2.4 (requires scanpy >=1.4.2).

    ]]></token>
  <token name="@INPUT_OPTS@">
    --input-format '${input_format}' input.h5
  </token>
  <token name="@OUTPUT_OPTS@">
#if str($output_format).startswith('anndata')
    --show-obj stdout --output-format anndata output.h5
#else
    --show-obj stdout --output-format loom output.h5
#end if
  </token>
  <token name="@PLOT_OPTS@">
#if $fig_title
    --title '${fig_title}'
#end if

  </token>
  <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="0.2.8">scanpy-scripts</requirement>
      <yield/>
    </requirements>
  </xml>

  <xml name="citations">

      }</citation>
    </citations>
  </xml>

  <xml name="input_object_params">
    <param name="input_obj_file" argument="input-object-file" type="data" format="h5,h5ad" label="Input object in AnnData/Loom format"/>
    <param name="input_format" argument="--input-format" type="select" label="Format of input object">
      <option value="anndata" selected="true">AnnData format hdf5</option>
      <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="output_plot_params">
    <param name="fig_title" argument="--title" type="text" label="Figure title"/>
    <param name="fig_size" argument="--fig-size" type="text" value="4,4" label="Figure size as 'width,height', e.g, '7,7'"/>