annotate scanpy_macros2.xml @ 27:3027cb62adbd draft default tip

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit ee197a80b2d591c393e1662854bc119b2ecab11e-dirty

<macros>
  <token name="@TOOL_VERSION@">1.9.3</token>
  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
  <token name="@PROFILE@">20.09</token>
  <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**
1.9.301+galaxy0: Moves to Scanpy 1.9.3

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.

1.8.1+1+galaxy0: Upate to scanpy-scripts 1.1.1 build 1 (running scanpy ==1.8.1), including improved Scrublet integration with batch handling.

1.8.1+galaxy0: Upate to scanpy-scripts 1.0.1 (running scanpy ==1.8.1), including Scrublet integration.

1.7.2+galaxy0: Upate to scanpy-scripts 0.3.3 (running scanpy ==1.7.2) to incorporate fix for object output from PAGA plotting, to allow PAGA init of FDG.

1.6.0+galaxy0: Update to scanpy-scripts 0.2.13 (running scanpy ==1.6.0) to incorporate new options, code simplifications, and batch integration methods. Jonathan Manning, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
EMBL-EBI https://www.ebi.ac.uk/

1.4.3+galaxy10: Update to scanpy-scripts 0.2.10 (running scanpy ==1.4.3) to address bugfixes in run-pca.

1.4.3+galaxy10: Update to scanpy-scripts 0.2.9 (running scanpy ==1.4.3) to address bugfixes in find-variable-genes.

1.4.3+galaxy10: Use profile 18.01 for modules.

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).

1.3.2+galaxy1: Normalise-data and filter-genes: Exposes ability to output 10x files.

1.3.2+galaxy0: Initial contribution. Ni Huang and Pablo Moreno, Expression Atlas team https://www.ebi.ac.uk/gxa/home  at
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 ${save_layer}
    #end if
  </token>
  <token name="@OUTPUT_OPTS@">
#if str($output_format).startswith('anndata')
    --show-obj stdout --output-format anndata output.h5
#else
    --show-obj stdout --output-format loom output.h5
#end if
  </token>
  <token name="@PLOT_OPTS@">
#if $fig_title
    --title '${fig_title}'
#end if
    --fig-size '${fig_size}'
    --fig-dpi ${fig_dpi}
    --fig-fontsize ${fig_fontsize}
    ${fig_frame}
    ./output.png
  </token>
  <token name="@EXPORT_MTX_OPTS@">${export_mtx}</token>

  <xml name="requirements">
    <requirements>
        <requirement type="package" version="1.9.301">scanpy-scripts</requirement>
      <yield/>
      <!-- use this format when you want to test against provisional conda artifacts
        <container type="docker">quay.io/biocontainers/scanpy-scripts:1.9.301  pyhdfd78af_0</container> 
      -->
    </requirements>
  </xml>

  <xml name="citations">
    <citations>
      <yield />
      <citation type="doi">10.1038/s41592-021-01102-w</citation>
      <citation type="doi">10.1186/s13059-017-1382-0</citation>
      <citation type="bibtex">
	@misc{githubscanpy-scripts,
	author = {Ni Huang, EBI Gene Expression Team},
	year = {2018},
	title = {Scanpy-scripts: command line interface for Scanpy},
	publisher = {GitHub},
	journal = {GitHub repository},
	url = {https://github.com/ebi-gene-expression-group/scanpy-scripts},
      }</citation>
      <citation type="doi">10.1101/2020.04.08.032698</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" 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">
    <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"/>
    <param name="fig_frame" type="boolean" truevalue="--frameon" falsevalue="--frameoff" checked="false"
           label="Show plot frame"/>
  </xml>

  <xml name="export_mtx_params">
    <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save to 10x mtx format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format."/>
  </xml>

  <xml name="export_mtx_outputs">
    <data name="matrix_10x" format="txt" from_work_dir="matrix.mtx" label="${tool.name} on ${on_string}: 10x matrix">
      <filter>export_mtx</filter>
    </data>
    <data name="genes_10x" format="tsv" from_work_dir="genes.tsv" label="${tool.name} on ${on_string}: 10x genes">
      <filter>export_mtx</filter>
    </data>
    <data name="barcodes_10x" format="tsv" from_work_dir="barcodes.tsv" label="${tool.name} on ${on_string}: 10x barcodes">
      <filter>export_mtx</filter>
    </data>
  </xml>
</macros>