comparison scanpy-plot-embedding.xml @ 4:109cfa259d8b draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003

3:b2410da4e381

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy1">
  <description>visualise cell embeddings</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    --legend-loc '${legend_loc}'
    --legend-fontsize '${legend_fontsize}'
#if $point_size
    --size ${point_size}
#end if
    @PLOT_OPTS@
]]></command>

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

    <param name="color_by" argument="--color" type="text" label="Color by attributes, comma separated texts">
      <sanitizer>
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/>
    <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">
      <option value="right margin" selected="true">Right margin</option>
      <option value="on data">On data</option>
    </param>

           help="Automatically determined if not specified."/>
    <expand macro="output_plot_params"/>
  </inputs>

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

  <tests>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>

4:109cfa259d8b

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy6">
  <description>visualise cell embeddings</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

    --legend-loc '${legend_loc}'
    --legend-fontsize '${legend_fontsize}'
#if $point_size
    --size ${point_size}
#end if
#if $gene_symbols_field
    --gene-symbols ${gene_symbols_field}
#end if
    @PLOT_OPTS@
]]></command>

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

    <param name="color_by" argument="--color" type="text" label="Color by attributes, comma separated texts">
      <sanitizer>
        <valid initial="string.printable"/>
      </sanitizer>
    </param>
    <param name="gene_symbols_field" argument="--gene-symbols" type="text" optional="true" label="Field for gene symbols" help="The field used in the AnnData object to store gene symbols, leave blank for the default (index), else a common value is 'gene_symbols'"/>
    <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/>
    <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">
      <option value="right margin" selected="true">Right margin</option>
      <option value="on data">On data</option>
    </param>

           help="Automatically determined if not specified."/>
    <expand macro="output_plot_params"/>
  </inputs>

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

  <tests>
    <test>
      <param name="input_obj_file" value="find_cluster.h5"/>