comparison scanpy-plot-trajectory.xml @ 11:c646bd10dcab draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"

10:c99f397434a3

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@">
  <description>visualise cell trajectories</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

  <inputs>
    <expand macro="input_object_params"/>
    <param name="use_key" argument="--use-key" type="text" value="paga"
           label="The key in `.uns` that contains trajectory information"/>
    <param name="layout" argument="--layout" type="select" label="Layout functions">
      <option value="fa" selected="true">ForceAtlas2</option>
      <option value="fr">Fruchterman-Reingold</option>
      <option value="rt">Reingold-Tilford</option>
    </param>
    <param name="basis" argument="--basis" type="text" optional="true" label="Name of the embedding to plot"
           help="Must be a key of `.obsm` without the prefix 'X_', e.g. 'umap'."/>
    <expand macro="output_plot_params"/>

    <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: trajectory plot"/>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="type" value="paga_compare"/>
      <output name="output_png" file="paga_compare.png" ftype="png" compare="sim_size"/>
    </test>
  </tests>

11:c646bd10dcab

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
  <description>visualise cell trajectories</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

  <inputs>
    <expand macro="input_object_params"/>
    <param name="use_key" argument="--use-key" type="text" value="paga"
           label="The key in `.uns` that contains trajectory information"/>
    <param name="layout" argument="--layout" type="select" label="Layout functions">
      <option value="fa">ForceAtlas2</option>
      <option value="fr" selected="true">Fruchterman-Reingold</option>
      <option value="rt">Reingold-Tilford</option>
    </param>
    <param name="basis" argument="--basis" type="text" optional="true" label="Name of the embedding to plot"
           help="Must be a key of `.obsm` without the prefix 'X_', e.g. 'umap'."/>
    <expand macro="output_plot_params"/>

    <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: trajectory plot"/>
  </outputs>

  <tests>
    <test>
      <param name="input_obj_file" value="paga.h5"/>
      <param name="input_format" value="anndata"/>
      <param name="type" value="paga_compare"/>
      <output name="output_png" file="paga_compare.png" ftype="png" compare="sim_size"/>
    </test>
  </tests>