Mercurial > repos > ebi-gxa > monocle3_plotcells

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/ commit b28c91675a0a90e45c65f275fc2fd596b431aa45"
author ebi-gxa
date Wed, 03 Jun 2020 14:57:57 -0400
parents 016c39d243fb
children
comparison
equal deleted inserted replaced
4:016c39d243fb 5:91980addce5e
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="monocle3_plotCells" name="Monocle3 plotCells" version="0.1.5+galaxy0" profile="@PROFILE@"> 2 <tool id="monocle3_plotCells" name="Monocle3 plotCells" version="0.1.5+galaxy1" profile="@PROFILE@">
3 <description> in the reduced dimensionality space</description> 3 <description> in the reduced dimensionality space</description>
4 <macros> 4 <macros>
5 <import>monocle3-macros.xml</import> 5 <import>monocle3-macros.xml</import>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="0.0.8">monocle3-cli</requirement> 8 <requirement type="package" version="0.0.9">monocle3-cli</requirement>
9 </requirements> 9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 LANG=en_US.UTF-8 monocle3 plotCells 11 LANG=en_US.UTF-8 monocle3 plotCells
12 --reduction-method '$(reduction_method)' 12 --reduction-method '$(reduction_method)'
13 --norm-method '$(norm_method)' 13 --norm-method '$(norm_method)'
63 <option value="tSNE">tSNE</option> 63 <option value="tSNE">tSNE</option>
64 <option value="PCA">PCA</option> 64 <option value="PCA">PCA</option>
65 <option value="LSI">LSI</option> 65 <option value="LSI">LSI</option>
66 </param> 66 </param>
67 <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}."/> 67 <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}."/>
68 <param name="genes" argument="--genes" optional="true" type="text" label="A list of gene IDs/short names to plot, one per panel."/> 68 <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`."/>
69 <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values for plotting."> 69 <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values for plotting.">
70 <option value="log" selected="true">Size factor correction and log transformation</option> 70 <option value="log" selected="true">Size factor correction and log transformation</option>
71 <option value="size_only">Size factor correction only</option> 71 <option value="size_only">Size factor correction only</option>
72 </param> 72 </param>
73 <param name="cell_size" argument="--cell-size" optional="true" type="float" value="1.5" label="The size of the point for each cell."/> 73 <param name="cell_size" argument="--cell-size" optional="true" type="float" value="1.5" label="The size of the point for each cell."/>