Mercurial > repos > ebi-gxa > scanpy_plot_trajectory

comparison scanpy-plot-trajectory.xml @ 16:5dde9b3c169e draft

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/tree/develop/tools/tertiary-analysis/scanpy commit 473f6f3175ac65391193d5671abaf1b560e4c593-dirty"
author ebi-gxa
date Tue, 23 Mar 2021 18:13:46 +0000
parents c646bd10dcab
children 2fe4b4cba312
comparison
equal deleted inserted replaced
15:3a00e9e50eb8 16:5dde9b3c169e
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
3 <description>visualise cell trajectories</description> 3 <description>visualise cell trajectories</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
10 PYTHONIOENCODING=utf-8 scanpy-cli plot paga 10 PYTHONIOENCODING=utf-8 scanpy-cli plot paga
11 #if $use_key 11 #if $use_key
12 --use-key '${use_key}' 12 --use-key '${use_key}'
13 #end if 13 #end if
14 --layout ${layout} 14 --layout ${layout}
15 --legend-loc '${legend_loc}'
15 #if $basis 16 #if $basis
16 --basis ${basis} 17 --basis ${basis}
17 #end if 18 #end if
18 #if $settings.default == "false" 19 #if $settings.default == "false"
19 --threshold ${settings.threshold} 20 --threshold ${settings.threshold}
47 label="The key in `.uns` that contains trajectory information"/> 48 label="The key in `.uns` that contains trajectory information"/>
48 <param name="layout" argument="--layout" type="select" label="Layout functions"> 49 <param name="layout" argument="--layout" type="select" label="Layout functions">
49 <option value="fa">ForceAtlas2</option> 50 <option value="fa">ForceAtlas2</option>
50 <option value="fr" selected="true">Fruchterman-Reingold</option> 51 <option value="fr" selected="true">Fruchterman-Reingold</option>
51 <option value="rt">Reingold-Tilford</option> 52 <option value="rt">Reingold-Tilford</option>
53 </param>
54 <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">
55 <option value="right margin" selected="true">Right margin</option>
56 <option value="on data">On data</option>
52 </param> 57 </param>
53 <param name="basis" argument="--basis" type="text" optional="true" label="Name of the embedding to plot" 58 <param name="basis" argument="--basis" type="text" optional="true" label="Name of the embedding to plot"
54 help="Must be a key of `.obsm` without the prefix 'X_', e.g. 'umap'."/> 59 help="Must be a key of `.obsm` without the prefix 'X_', e.g. 'umap'."/>
55 <expand macro="output_plot_params"/> 60 <expand macro="output_plot_params"/>
56 <conditional name="settings"> 61 <conditional name="settings">