comparison scanpy-plot-embedding.xml @ 3:b2410da4e381 draft

planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604

2:882f4671d686

<?xml version="1.0" encoding="utf-8"?>
<tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy0">
  <description>visualise cell embeddings</description>
  <macros>
    <import>scanpy_macros2.xml</import>
  </macros>
  <expand macro="requirements"/>

]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <param name="basis" argument="--basis" type="text" label="Name of the embedding to plot"/>
    <param name="color_by" argument="--color" type="text" label="Color by attributes, comma separated texts"/>
    <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>

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"/>

]]></command>

  <inputs>
    <expand macro="input_object_params"/>
    <param name="basis" argument="--basis" type="text" label="Name of the embedding to plot"/>
    <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>