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comparison scanpy-run-fdg.xml @ 0:96af0059b974 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 4846776f55931e176f7e77af7c185ec6fec7d142"
author ebi-gxa
date Mon, 16 Sep 2019 08:23:52 -0400
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-1:000000000000 0:96af0059b974
1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy0">
3 <description>visualise cell clusters using force-directed graph</description>
4 <macros>
5 <import>scanpy_macros2.xml</import>
6 </macros>
7 <expand macro="requirements"/>
8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-cli embed fdg
11 --use-graph '${use_graph}'
12 --key-added '${key_added}'
13 #if $embeddings
14 --export-embedding embeddings.csv
15 #end if
16 #if $settings.default == "false"
17 --random-state ${settings.random_seed}
18 --layout ${settings.layout}
19 #if $settings.init_pos
20 --init-pos '${settings.init_pos}'
21 #end if
22 #end if
23 @INPUT_OPTS@
24 @OUTPUT_OPTS@
25
26 ]]></command>
27
28 <inputs>
29 <expand macro="input_object_params"/>
30 <expand macro="output_object_params"/>
31 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/>
32 <param name="use_graph" argument="--use-graph" value="neighbors" type="text"
33 label="Name of the slot that holds the KNN graph"/>
34 <param name="key_added" argument="--key-added" type="text" optional="true"
35 label="Additional suffix to the name of the slot to save the embedding"/>
36
37 <conditional name="settings">
38 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
39 <when value="true"/>
40 <when value="false">
41 <param name="init_pos" argument="--init-pos" type="text" label="Method to initialise embedding, any key for adata.obsm or choose from the preset methods">
42 <option value="paga">paga</option>
43 </param>
44 <param name="layout" argument="--layout" type="select" label="Graph layout">
45 <option value="fa" selected="true">fa</option>
46 <option value="fr">fr</option>
47 <option value="grid_fr">grid fr</option>
48 </param>
49 <param name="random_seed" argument="--random-state" type="integer" value="0" label="Seed for numpy random number generator"/>
50 </when>
51 </conditional>
52 </inputs>
53
54 <outputs>
55 <data name="output_h5" format="h5" from_work_dir="output.h5" label="${tool.name} on ${on_string}: FDG object"/>
56 <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: FDG embeddings">
57 <filter>embeddings</filter>
58 </data>
59 </outputs>
60
61 <tests>
62 <test>
63 <param name="input_obj_file" value="find_cluster.h5"/>
64 <param name="input_format" value="anndata"/>
65 <param name="output_format" value="anndata"/>
66 <param name="default" value="false"/>
67 <param name="embeddings" value="true"/>
68 <param name="random_seed" value="0"/>
69 <output name="output_h5" file="run_fdg.h5" ftype="h5" compare="sim_size"/>
70 <output name="output_embed" file="run_fdg.embeddings.csv" ftype="csv" compare="sim_size">
71 <assert_contents>
72 <has_n_columns n="2" sep=","/>
73 </assert_contents>
74 </output>
75 </test>
76 </tests>
77
78 <help><![CDATA[
79 ================================================================================
80 Embed the neighborhood graph using Force-directed Graph (`scanpy.tl.draw_graph`)
81 ================================================================================
82
83 For making FDG plots, please use `Scanpy PlotEmbed` with the output of this
84 tool and enter "draw_graph_{layout}" as the name of the embedding to plot.
85
86 It yields `X_draw_graph_{layout}`, FDG coordinates of data.
87
88 @HELP@
89
90 @VERSION_HISTORY@
91 ]]></help>
92 <expand macro="citations"/>
93 </tool>