comparison monocle3-plotCells.xml @ 5:91980addce5e draft default tip

"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b28c91675a0a90e45c65f275fc2fd596b431aa45"

4:016c39d243fb

<?xml version="1.0" encoding="utf-8"?>
<tool id="monocle3_plotCells" name="Monocle3 plotCells" version="0.1.5+galaxy0" profile="@PROFILE@">
  <description> in the reduced dimensionality space</description>
  <macros>
    <import>monocle3-macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package" version="0.0.8">monocle3-cli</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
LANG=en_US.UTF-8 monocle3 plotCells
    --reduction-method '$(reduction_method)'
    --norm-method '$(norm_method)'

      <option value="tSNE">tSNE</option>
      <option value="PCA">PCA</option>
      <option value="LSI">LSI</option>
    </param>
    <param name="color_cells_by" argument="--color-cells-by" optional="true" type="text" value="pseudotime" label="The cell attribute (e.g. the column of pData(cds)) to map to each cell's color, or one of {cluster, partition, pseudotime}."/>
    <param name="genes" argument="--genes" optional="true" type="text" label="A list of gene IDs/short names to plot, one per panel."/>
    <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values for plotting.">
      <option value="log" selected="true">Size factor correction and log transformation</option>
      <option value="size_only">Size factor correction only</option>
    </param>
    <param name="cell_size" argument="--cell-size" optional="true" type="float" value="1.5" label="The size of the point for each cell."/>

5:91980addce5e

<?xml version="1.0" encoding="utf-8"?>
<tool id="monocle3_plotCells" name="Monocle3 plotCells" version="0.1.5+galaxy1" profile="@PROFILE@">
  <description> in the reduced dimensionality space</description>
  <macros>
    <import>monocle3-macros.xml</import>
  </macros>
  <requirements>
    <requirement type="package" version="0.0.9">monocle3-cli</requirement>
  </requirements>
  <command detect_errors="exit_code"><![CDATA[
LANG=en_US.UTF-8 monocle3 plotCells
    --reduction-method '$(reduction_method)'
    --norm-method '$(norm_method)'

      <option value="tSNE">tSNE</option>
      <option value="PCA">PCA</option>
      <option value="LSI">LSI</option>
    </param>
    <param name="color_cells_by" argument="--color-cells-by" optional="true" type="text" value="pseudotime" label="The cell attribute (e.g. the column of pData(cds)) to map to each cell's color, or one of {cluster, partition, pseudotime}."/>
    <param name="genes" argument="--genes" optional="true" type="text" label="A list of gene IDs/short names to plot." help="For adding more than one gene, write them as a comma separated list, with no spaces in the middle, like `crp1,crp2,cycX`."/>
    <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values for plotting.">
      <option value="log" selected="true">Size factor correction and log transformation</option>
      <option value="size_only">Size factor correction only</option>
    </param>
    <param name="cell_size" argument="--cell-size" optional="true" type="float" value="1.5" label="The size of the point for each cell."/>