Mercurial > repos > ebi-gxa > scanpy_plot_trajectory

comparison scanpy-plot-trajectory.xml @ 17:2fe4b4cba312 draft

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"planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 858a2398f1dbbd60110867c593c237358c794615-dirty"
author ebi-gxa
date Mon, 12 Apr 2021 14:44:49 +0000
parents 5dde9b3c169e
children f489ccdd423c
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16:5dde9b3c169e 17:2fe4b4cba312
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@+galaxy1" profile="@PROFILE@"> 2 <tool id="scanpy_plot_trajectory" name="Scanpy PlotTrajectory" version="@TOOL_VERSION@+galaxy0" 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"/>
36 #end if 36 #end if
37 #if $settings.edge_width 37 #if $settings.edge_width
38 --edge-width-scale ${settings.edge_width} 38 --edge-width-scale ${settings.edge_width}
39 #end if 39 #end if
40 #end if 40 #end if
41 #if str($output_format).startswith('anndata')
42 --show-obj stdout --output-format anndata --output-obj output.h5
43 #else
44 --show-obj stdout --output-format loom --output-obj output.h5
45 #end if
41 @INPUT_OPTS@ 46 @INPUT_OPTS@
42 @PLOT_OPTS@ 47 @PLOT_OPTS@
43 ]]></command> 48 ]]></command>
44 49
45 <inputs> 50 <inputs>
46 <expand macro="input_object_params"/> 51 <expand macro="input_object_params"/>
52 <expand macro="output_object_params"/>
47 <param name="use_key" argument="--use-key" type="text" value="paga" 53 <param name="use_key" argument="--use-key" type="text" value="paga"
48 label="The key in `.uns` that contains trajectory information"/> 54 label="The key in `.uns` that contains trajectory information"/>
49 <param name="layout" argument="--layout" type="select" label="Layout functions"> 55 <param name="layout" argument="--layout" type="select" label="Layout functions">
50 <option value="fa">ForceAtlas2</option> 56 <option value="fa">ForceAtlas2</option>
51 <option value="fr" selected="true">Fruchterman-Reingold</option> 57 <option value="fr" selected="true">Fruchterman-Reingold</option>
83 </when> 89 </when>
84 </conditional> 90 </conditional>
85 </inputs> 91 </inputs>
86 92
87 <outputs> 93 <outputs>
94 <expand macro="output_data_obj" description="Plotted PAGA"/>
88 <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: trajectory plot"/> 95 <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: trajectory plot"/>
89 </outputs> 96 </outputs>
90 97
91 <tests> 98 <tests>
92 <test> 99 <test>
93 <param name="input_obj_file" value="paga.h5"/> 100 <param name="input_obj_file" value="paga.h5"/>
94 <param name="input_format" value="anndata"/> 101 <param name="input_format" value="anndata"/>
102 <param name="output_format" value="anndata"/>
95 <param name="type" value="paga_compare"/> 103 <param name="type" value="paga_compare"/>
104 <output name="output_h5" file="plotted_paga.h5" ftype="h5" compare="sim_size"/>
96 <output name="output_png" file="paga_compare.png" ftype="png" compare="sim_size"/> 105 <output name="output_png" file="paga_compare.png" ftype="png" compare="sim_size"/>
97 </test> 106 </test>
98 </tests> 107 </tests>
99 108
100 <help><![CDATA[ 109 <help><![CDATA[