<macros>
  <xml name="requirements">
    <requirements>
      <requirement type="package" version="@TOOL_VERSION@">sccaf</requirement>
    </requirements>
  </xml>
  <token name="@TOOL_VERSION@">0.0.7</token>
  <token name="@SCCAF_INTRO@">
SCCAF explained
===============

Single Cell Clustering Assessment Framework (SCCAF) is a novel method for
automated identification of putative cell types from single cell RNA-seq
(scRNA-seq) data. By iteratively applying clustering and a machine learning
approach to gene expression profiles of a given set of cells, SCCAF
simultaneously identifies distinct cell groups and a weighted list of feature
genes for each group. The feature genes, which are overexpressed in the
particular cell group, jointly discriminate the given cell group from other
cells. Each such group of cells corresponds to a putative cell type or state,
characterised by the feature genes as markers.
  </token>
  <token name="@HELP@">More information can be found at https://github.com/SCCAF/SCCAF</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.show_edges
                  --edges
    #end if
    #if $do_plotting.show_arrows
                  --arrows
    #end if
    #if not $do_plotting.color_order
                  --no-sort-order
    #end if
    #if $do_plotting.omit_frame
                  --frameoff
    #end if
#end if
  </token>
  <xml name="citations">
    <citations>
      <citation type="doi"></citation>
      <citation type="bibtex">
	@misc{githubsccaf,
	author = {Miao, Zhichao},
	year = {2018},
	title = {SCCAF},
	publisher = {GitHub},
	journal = {GitHub repository},
	url = {https://github.com/Functional-Genomics/SCCAF},
      }</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 AnnData hdf5 format" help="Normally the result of Scanpy (or equivalent), which already has both a visualisation (either tSNE, UMAP or PCA - needed) and clustering (ideally) pre-computed."/>
    <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="show_edges" argument="--edges" type="boolean" checked="false" label="Show edges"/>
    <param name="show_arrows" argument="--arrows" type="boolean" checked="false" label="Show arrows"/>
    <param name="color_order" argument="--no-sort-order" type="boolean" checked="true" label="Element with high color-by value plot on top"/>
    <param name="omit_frame" argument="--frameoff" type="boolean" checked="false" label="Show frame"/>
  </xml>
</macros>