comparison scanpy_macros2.xml @ 6:5bb009f95e03 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ebe77c8718ec65277f4dc0d71fa5f4c5677df62d-dirty"

5:b202e078a83f

EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
    ]]></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

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

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="0.3.3">scanpy-scripts</requirement>
      <yield/>
    </requirements>
  </xml>

  <xml name="citations">

    <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'"/>
    <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
    <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>

6:5bb009f95e03

EMBL-EBI https://www.ebi.ac.uk/ and Teichmann Lab at Wellcome Sanger Institute.
    ]]></token>
  <token name="@INPUT_OPTS@">
    --input-format '${input_format}' input.h5
  </token>
  <token name="@SAVE_MATRIX_OPTS@">
    #if $save_raw
      --save-raw
    #end if
    #if $save_layer
      --save-layer ${settings.save_layer}
    #end if
  </token>
  <token name="@OUTPUT_OPTS@">
#if str($output_format).startswith('anndata')
    --show-obj stdout --output-format anndata output.h5
#else
    --show-obj stdout --output-format loom output.h5

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

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="0.4.0">scanpy-scripts</requirement>
      <yield/>
    </requirements>
  </xml>

  <xml name="citations">

    <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">
    <param name="save_raw" argument="--save-raw" type="boolean" truevalue="yes" falsevalue="no" checked="false"
      label="Save adata to adata.raw before processing?" />
    <param name="save_layer" argument="--save-layer" type="text" optional="true"
      label="Save adata.X to the specified layer before processing."/>
  </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'"/>
    <param name="fig_dpi" argument="--fig-dpi" type="integer" min="1" value="80" label="Figure dpi"/>
    <param name="fig_fontsize" argument="--fig-fontsize" type="integer" min="0" value="10" label="Figure font size"/>