annotate scanpy_macros.xml @ 0:34d65f2ccde3 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 4846776f55931e176f7e77af7c185ec6fec7d142"

<macros>
  <token name="@TOOL_VERSION@">1.3.2</token>
  <token name="@HELP@">More information can be found at https://scanpy.readthedocs.io</token>
  <token name="@PLOT_OPTS@">
#if $do_plotting.plot
                  -P output.png
                  --projectio $do_plotting.projection
                  --components $do_plotting.components
    #if $do_plotting.color_by
                  --color-by $do_plotting.color_by
    #end if
    #if $do_plotting.groups
                  --group $do_plotting.groups
    #end if
    #if $do_plotting.use_raw
                  --use-raw
    #end if
    #if $do_plotting.palette
                  --palette $do_plotting.palette
    #end if
    #if $do_plotting.edges
                  --edges
    #end if
    #if $do_plotting.arrows
                  --arrows
    #end if
    #if not $do_plotting.sort_order
                  --no-sort-order
    #end if
    #if $do_plotting.frameoff
                  --frameoff
    #end if
#end if
  </token>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="0.0.5">scanpy-scripts</requirement>
      <yield/>
    </requirements>
  </xml>
  <token name="@EXPORT_MTX_OPTS@">
      ${export_mtx}
  </token>
  <token name="@VERSION_HISTORY@"><![CDATA[
**Version history**

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>
  <xml name="citations">
    <citations>
      <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>
      <yield />
    </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, current support is incomplete</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, current support is defective</option>
    </param>
  </xml>
  <xml name="output_plot_params">
    <param name="color_by" argument="--color-by" type="text" value="n_genes" label="Color by attributes, comma separated strings"/>
    <param name="groups" argument="--groups" type="text" optional="ture" label="Restrict plotting to named groups, comma separated strings"/>
    <param name="projection" argument="--projection" type="select" label="Plot projection">
      <option value="2d" selected="true">2D</option>
      <option value="3d">3D</option>
    </param>
    <param name="components" argument="--components" type="text" value="1,2" label="Components to plot, comma separated integers"/>
    <param name="palette" argument="--palette" type="text" optional="true" label="Palette"/>
    <param name="use_raw" argument="--use-raw" type="boolean" checked="false" label="Use raw attributes if present"/>
    <param name="edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
    <param name="arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
    <param name="sort_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
    <param name="frameoff" argument="--frameoff" type="boolean" checked="false" label="Omit frame"/>
  </xml>
  <xml name="export_mtx_params">
    <param name="export_mtx" argument="--export-mtx" type="boolean" truevalue="--export-mtx ./" falsevalue="" checked="false" label="Save normalised data to 10x format" help="If enabled, it will generate in addition to the main output in Loom or AnnData an export in 10x format of the normalised data."/>
  </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>