Mercurial > repos > ebi-gxa > monocle3_plotcells

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

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"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
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1 <?xml version="1.0" encoding="utf-8"?>
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2 <tool id="monocle3_plotCells" name="Monocle3 plotCells" version="0.1.5+galaxy1" profile="@PROFILE@">
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3 <description> in the reduced dimensionality space</description>
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4 <macros>
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5 <import>monocle3-macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="0.0.9">monocle3-cli</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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11 LANG=en_US.UTF-8 monocle3 plotCells
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12 --reduction-method '$(reduction_method)'
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13 --norm-method '$(norm_method)'
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14 #if $xdim
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15 --xdim '$(xdim)'
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16 #end if
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17 #if $ydim
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18 --ydim '$(ydim)'
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19 #end if
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20 #if $color_cells_by
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21 --color-cells-by '$(color_cells_by)'
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22 #end if
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23 #if $genes
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24 --genes '$(genes)'
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25 #end if
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26 #if $cell_size
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27 --cell-size '$(cell_size)'
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28 #end if
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29 #if $alpha
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30 --alpha '$(alpha)'
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31 #end if
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32 #if $label_cell_groups
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33 --label-cell-groups
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34 #end if
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35 #if $no_trajectory_graph
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36 --no-trajectory-graph
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37 #end if
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38 #if $label_groups_by_cluster
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39 --label-groups-by-cluster
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40 #end if
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41 #if $label_leaves
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42 --label-leaves
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43 #end if
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44 #if $label_roots
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45 --label-roots
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46 #end if
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47 #if $label_branch_points
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48 --label-branch-points
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49 #end if
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50
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51 @INPUT_OPTS@
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52 output.png
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53
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54 @VERBOSE@
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55 ]]></command>
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56
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57 <inputs>
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58 <expand macro="input_object_params"/>
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59 <param name="xdim" argument="--xdim" optional="true" type="integer" value="1" label="The column of reducedDimS(cds) to plot on the horizontal axis."/>
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60 <param name="ydim" argument="--ydim" optional="true" type="integer" value="2" label="The column of reducedDimS(cds) to plot on the vertical axis."/>
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61 <param name="reduction_method" argument="--reduction-method" type="select" label="The dimensionality reduction for plotting.">
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62 <option value="UMAP" selected="true">UMAP</option>
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63 <option value="tSNE">tSNE</option>
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64 <option value="PCA">PCA</option>
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65 <option value="LSI">LSI</option>
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66 </param>
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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}."/>
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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`."/>
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69 <param name="norm_method" argument="--norm-method" type="select" label="Determines how to transform expression values for plotting.">
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70 <option value="log" selected="true">Size factor correction and log transformation</option>
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71 <option value="size_only">Size factor correction only</option>
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72 </param>
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73 <param name="cell_size" argument="--cell-size" optional="true" type="float" value="1.5" label="The size of the point for each cell."/>
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74 <param name="alpha" argument="--alpha" optional="true" type="float" value="1" label="The alpha aesthetics for the original cell points, useful to highlight the learned principal graph."/>
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75 <param name="label_cell_groups" argument="--label-cell-groups" type="boolean" checked="true" label="If set, display the cell group names directly on the plot. Otherwise include a color legend on the side of the plot."/>
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76 <param name="no_trajectory_graph" argument="--no-trajectory-graph" type="boolean" checked="false" label="When this option is set, skip displaying the trajectory graph inferred by learn_graph()."/>
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77 <param name="label_groups_by_cluster" argument="--label-groups-by-cluster" type="boolean" checked="false" label="If set, and setting --color-cells-by to something other than cluster, label the cells of each cluster independently. Can result in duplicate labels being present in the manifold."/>
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78 <param name="label_leaves" argument="--label-leaves" type="boolean" checked="false" label="If set, label the leaves of the principal graph."/>
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79 <param name="label_roots" argument="--label-roots" type="boolean" checked="false" label="If set, label the roots of the principal graph."/>
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80 <param name="label_branch_points" argument="--label-branch-points" type="boolean" checked="false" label="If set, label the branch points of the principal graph."/>
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81 <expand macro="verbose_flag"/>
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82 </inputs>
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83
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84 <outputs>
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85 <data name="output_tsv" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: png"/>
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86 </outputs>
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87
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88 <tests>
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89 <test>
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90 <param name="input_object_file" value="input.RDS"/>
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91 <param name="input_object_format" value="cds3"/>
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92 <param name="reduction_method" value="UMAP"/>
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93 <param name="xdim" value="1"/>
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94 <param name="ydim" value="2"/>
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95 <param name="color_cells_by" value="pseudotime"/>
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96 <param name="norm_method" value="log"/>
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97 <param name="cell_size" value="1.5"/>
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98 <param name="alpha" value="1"/>
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99 <output name="output_tsv" file="output.tsv" ftype="tsv" compare="sim_size"/>
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100 </test>
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101 </tests>
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102
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103 <help><![CDATA[
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104 =====================================
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105 Monocle3 cell plotting (`plot_cells`)
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106 =====================================
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107
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108 Display various information about cells (clustering, pseudotime, the inferred graph,
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109 user-provided annotations, gene expression) in reduced dimensions.
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110
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111 @HELP@
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112
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113 @VERSION_HISTORY@
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114 ]]></help>
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115 <expand macro="citations"/>
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116 </tool>