comparison scanpy_macros2.xml @ 14:ff6decc0f432 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

13:e9788746e0f6

<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.

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

  <xml name="requirements">
    <requirements>
      <requirement type="package" version="1.1.6">scanpy-scripts</requirement>
      <yield/>
    </requirements>
  </xml>

  <xml name="citations">
    <citations>
      <yield />
      <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},

	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>
      <citation type="doi">10.1038/s41592-021-01102-w</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"/>

14:ff6decc0f432

<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.

  </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},

	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"/>