comparison scanpy-plot-trajectory.xml @ 17:2fe4b4cba312 draft

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"

16:5dde9b3c169e

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
  <description>visualise cell trajectories</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    #end if
    #if $settings.edge_width
        --edge-width-scale ${settings.edge_width}
    #end if
#end if
    @INPUT_OPTS@
    @PLOT_OPTS@
]]></command>

  <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>

      </when>
    </conditional>
  </inputs>

  <outputs>
    <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>

  <help><![CDATA[

17:2fe4b4cba312

<?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"/>

    #end if
    #if $settings.edge_width
        --edge-width-scale ${settings.edge_width}
    #end if
#end if
    #if str($output_format).startswith('anndata')
        --show-obj stdout --output-format anndata --output-obj output.h5
    #else
        --show-obj stdout --output-format loom --output-obj output.h5
    #end if
    @INPUT_OPTS@
    @PLOT_OPTS@
]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <expand macro="output_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>

      </when>
    </conditional>
  </inputs>

  <outputs>
    <expand macro="output_data_obj" description="Plotted PAGA"/>
    <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="output_format" value="anndata"/>
      <param name="type" value="paga_compare"/>
      <output name="output_h5" file="plotted_paga.h5" ftype="h5" compare="sim_size"/>
      <output name="output_png" file="paga_compare.png" ftype="png" compare="sim_size"/>
    </test>
  </tests>

  <help><![CDATA[