Mercurial > repos > ebi-gxa > scanpy_run_fdg

comparison scanpy-run-fdg.xml @ 11:dd27b39c5c12 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 62f47287c7e8449c59a1f1f454852ddc669b1b1e-dirty"
author ebi-gxa
date Mon, 07 Sep 2020 13:09:43 +0000
parents 425f2e046231
children a6190ae4fe16
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10:4722394f6af9 11:dd27b39c5c12
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> 2 <tool id="scanpy_run_fdg" name="Scanpy RunFDG" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>visualise cell clusters using force-directed graph</description> 3 <description>visualise cell clusters using force-directed graph</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"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '${input_obj_file}' input.h5 && 9 ln -s '${input_obj_file}' input.h5 &&
10 PYTHONIOENCODING=utf-8 scanpy-cli embed fdg 10 PYTHONIOENCODING=utf-8 scanpy-cli embed fdg
11 --use-graph '${use_graph}' 11 --key-added-ext '${key_added_ext}'
12 --key-added '${key_added}'
13 #if $embeddings 12 #if $embeddings
14 --export-embedding embeddings.csv 13 --export-embedding embeddings.tsv
15 #end if 14 #end if
16 #if $settings.default == "false" 15 #if $settings.default == "false"
16 #if $settings.neighbors_key
17 --neighbors-key '${settings.neighbors_key}'
18 #end if
19 #if $settings.obsp
20 --obsp '${settings.obsp}'
21 #end if
17 --random-state ${settings.random_seed} 22 --random-state ${settings.random_seed}
18 --layout ${settings.layout} 23 --layout ${settings.layout}
19 #if $settings.init_pos 24 #if $settings.init_pos
20 --init-pos '${settings.init_pos}' 25 --init-pos '${settings.init_pos}'
26 #end if
27 #if $settings.root
28 --root '${settings.root}'
21 #end if 29 #end if
22 #end if 30 #end if
23 @INPUT_OPTS@ 31 @INPUT_OPTS@
24 @OUTPUT_OPTS@ 32 @OUTPUT_OPTS@
25 33
26 ]]></command> 34 ]]></command>
27 35
28 <inputs> 36 <inputs>
29 <expand macro="input_object_params"/> 37 <expand macro="input_object_params"/>
30 <expand macro="output_object_params"/> 38 <expand macro="output_object_params"/>
31 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in csv format"/> 39 <param name="embeddings" type="boolean" checked="true" label="Output embeddings in tsv format"/>
32 <param name="use_graph" argument="--use-graph" value="neighbors" type="text" 40 <param name="key_added_ext" argument="--key-added-ext" type="text" optional="true"
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"/> 41 label="Additional suffix to the name of the slot to save the embedding"/>
36 42
37 <conditional name="settings"> 43 <conditional name="settings">
38 <param name="default" type="boolean" checked="true" label="Use programme defaults"/> 44 <param name="default" type="boolean" checked="true" label="Use programme defaults"/>
39 <when value="true"/> 45 <when value="true"/>
40 <when value="false"> 46 <when value="false">
47 <param name="neighbors_key" argument="--neighbors-key" value="neighbors" type="text"
48 label="Name of the slot that holds the KNN graph"/>
49 <param name="obsp" type="boolean" checked="false" label="Use .obsp[obsp] as adjacency" help="You can’t specify both obsp and neighbors-key at the same time."/>
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"> 50 <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> 51 <option value="paga">paga</option>
43 </param> 52 </param>
44 <param name="layout" argument="--layout" type="select" label="Graph layout"> 53 <param name="layout" argument="--layout" type="select" label="Graph layout">
45 <option value="fa" selected="true">fa</option> 54 <option value="fa">fa</option>
46 <option value="fr">fr</option> 55 <option value="fr" selected="true">fr</option>
47 <option value="grid_fr">grid fr</option> 56 <option value="grid_fr">grid fr</option>
57 <option value="kk">kk</option>
58 <option value="lgl">lgl</option>
59 <option value="drl">drl</option>
60 <option value="rt">rt</option>
61 <option value="rt_circular">rt_circular</option>
48 </param> 62 </param>
63 <param name="root" argument="--root" type="integer" optional="true" label="Root for tree layouts"/>
49 <param name="random_seed" argument="--random-state" type="integer" value="0" label="Seed for numpy random number generator"/> 64 <param name="random_seed" argument="--random-state" type="integer" value="0" label="Seed for numpy random number generator"/>
50 </when> 65 </when>
51 </conditional> 66 </conditional>
52 </inputs> 67 </inputs>
53 68
54 <outputs> 69 <outputs>
55 <expand macro="output_data_obj" description="FDG object"/> 70 <expand macro="output_data_obj" description="FDG object"/>
56 <data name="output_embed" format="csv" from_work_dir="embeddings.csv" label="${tool.name} on ${on_string}: FDG embeddings"> 71 <data name="output_embed" format="tabular" from_work_dir="embeddings.tsv" label="${tool.name} on ${on_string}: FDG embeddings">
57 <filter>embeddings</filter> 72 <filter>embeddings</filter>
58 </data> 73 </data>
59 </outputs> 74 </outputs>
60 75
61 <tests> 76 <tests>
65 <param name="output_format" value="anndata"/> 80 <param name="output_format" value="anndata"/>
66 <param name="default" value="false"/> 81 <param name="default" value="false"/>
67 <param name="embeddings" value="true"/> 82 <param name="embeddings" value="true"/>
68 <param name="random_seed" value="0"/> 83 <param name="random_seed" value="0"/>
69 <output name="output_h5" file="run_fdg.h5" ftype="h5" compare="sim_size"/> 84 <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"> 85 <output name="output_embed" file="run_fdg.embeddings.tsv" ftype="tabular" compare="sim_size">
71 <assert_contents> 86 <assert_contents>
72 <has_n_columns n="2" sep=","/> 87 <has_n_columns n="3"/>
73 </assert_contents> 88 </assert_contents>
74 </output> 89 </output>
75 </test> 90 </test>
76 </tests> 91 </tests>
77 92