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comparison scanpy-plot-embedding.xml @ 11:f48cfaa2e515 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 14:02:08 +0000
parents 210026a1a50a
children 9fafbfcdee0d
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10:068c4bf0e0db 11:f48cfaa2e515
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy10" profile="@PROFILE@"> 2 <tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
3 <description>visualise cell embeddings</description> 3 <description>visualise cell embeddings</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 plot embed 10 PYTHONIOENCODING=utf-8 scanpy-cli plot embed
11 @INPUT_OPTS@ 11 @INPUT_OPTS@
12 --basis '${basis}' 12 #if $color_by
13 --color '${color_by}' 13 --color '${color_by}'
14 ${use_raw} 14 #end if
15 ${use_raw}
15 --legend-loc '${legend_loc}' 16 --legend-loc '${legend_loc}'
16 --legend-fontsize '${legend_fontsize}' 17 --legend-fontsize '${legend_fontsize}'
18 #if $basis
19 --basis '${basis}'
20 #end if
21 #if $groups
22 --groups $groups
23 #end if
24 #if $neighbors_key
25 --neighbors-key '${neighbors_key}'
26 #end if
27 #if $layer
28 --layer '${layer}'
29 #end if
17 #if $point_size 30 #if $point_size
18 --size ${point_size} 31 --size ${point_size}
19 #end if 32 #end if
20 #if $gene_symbols_field 33 #if $gene_symbols_field
21 --gene-symbols ${gene_symbols_field} 34 --gene-symbols ${gene_symbols_field}
35 #end if
36 ${edges} --edges-width ${edges_width}
37 #if $edges_color
38 --edges-color ${edges_color}
22 #end if 39 #end if
23 @PLOT_OPTS@ 40 #if $components
41 --components ${components}
42 #end if
43 --projection $projection
44 $sort_order
45 @PLOT_OPTS@
24 ]]></command> 46 ]]></command>
25 47
26 <inputs> 48 <inputs>
27 <expand macro="input_object_params"/> 49 <expand macro="input_object_params"/>
28 <param name="basis" argument="--basis" type="text" label="Name of the embedding to plot"/> 50 <param name="basis" argument="--basis" type="text" value='umap' label="name of the embedding to plot"/>
29 <param name="color_by" argument="--color" type="text" label="Color by attributes, comma separated texts"> 51 <param name="color_by" argument="--color" type="text" label="color by attributes, comma separated texts">
30 <sanitizer> 52 <sanitizer>
31 <valid initial="string.printable"/> 53 <valid initial="string.printable"/>
32 </sanitizer> 54 </sanitizer>
33 </param> 55 </param>
56 <param name="groups" argument="--groups" type="text" value="" label="Key for categorical in `.obs`" help="You can pass your predefined groups by choosing any categorical annotation of observations."/>
34 <param name="gene_symbols_field" argument="--gene-symbols" type="text" optional="true" label="Field for gene symbols" help="The field used in the AnnData object to store gene symbols, leave blank for the default (index), else a common value is 'gene_symbols'"/> 57 <param name="gene_symbols_field" argument="--gene-symbols" type="text" optional="true" label="Field for gene symbols" help="The field used in the AnnData object to store gene symbols, leave blank for the default (index), else a common value is 'gene_symbols'"/>
35 <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/> 58 <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/>
59 <param name="layer" argument="--layer" value="" type="text"
60 label="Name of the AnnData object layer to plot" help="By default adata.raw.X is plotted. If use_raw=False is set, then adata.X is plotted. If layer is set to a valid layer name, then the layer is plotted. layer takes precedence over use_raw." />
61 <param name="neighbors_key" argument="--neighbors-key" value="" type="text"
62 label="Where to look for neighbors connectivities." help="If not specified, this looks in .obsp[‘connectivities’] for connectivities (default storage place for pp.neighbors). If specified, this looks .obsp[.uns[neighbors_key][‘connectivities_key’]] for connectivities."/>
36 <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend"> 63 <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend">
37 <option value="right margin" selected="true">Right margin</option> 64 <option value="right margin" selected="true">Right margin</option>
38 <option value="on data">On data</option> 65 <option value="on data">On data</option>
39 </param> 66 </param>
40 <param name="legend_fontsize" argument="--legend-fontsize" type="integer" value="15" label="Legend font size"/> 67 <param name="legend_fontsize" argument="--legend-fontsize" type="integer" value="15" label="Legend font size"/>
41 <param name="point_size" argument="--size" type="integer" optional="true" label="Point size" 68 <param name="point_size" argument="--size" type="integer" optional="true" label="Point size"
42 help="Automatically determined if not specified."/> 69 help="Automatically determined if not specified."/>
70 <param name="edges" argument="--edges" type="boolean" checked="False" truevalue="--edges" falsevalue="" label="Show edges?"/>
71 <param name="edges_width" argument="--edges-width" type="float" value="0.1" label="Width of edges"/>
72 <param name="edges_color" argument="--edges-color" type="text" value="" label="Color of edges"/>
73 <param name="sort_order" argument="--no-sort-order" type="boolean" checked="False" truevalue="" falsevalue="--no-sort-order" label="Plot in order?" help="For continuous annotations used as 'color parameter, plot data points with higher values on top of others."/>
74 <param name="components" argument="--components" type="text" value="" label="Components to plot" help="Comma-separated list, e.g. '1,2', '2,3'. To plot all available components use 'all'."/>
75 <param name="projection" argument="--projection" type="select" label="Plot projection">
76 <option value="2d" selected="true">2D</option>
77 <option value="3d">3D</option>
78 </param>
43 <expand macro="output_plot_params"/> 79 <expand macro="output_plot_params"/>
44 </inputs> 80 </inputs>
45 81
46 <outputs> 82 <outputs>
47 <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: ${basis} embedding plot"/> 83 <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: ${basis} embedding plot"/>
49 85
50 <tests> 86 <tests>
51 <test> 87 <test>
52 <param name="input_obj_file" value="find_cluster.h5"/> 88 <param name="input_obj_file" value="find_cluster.h5"/>
53 <param name="input_format" value="anndata"/> 89 <param name="input_format" value="anndata"/>
90 <param name="basis" value="X_pca"/>
54 <param name="color_by" value="louvain"/> 91 <param name="color_by" value="louvain"/>
55 <output name="output_png" file="run_tsne.png" ftype="png" compare="sim_size"/> 92 <output name="output_png" file="plot_embed.png" ftype="png" compare="sim_size"/>
56 </test> 93 </test>
57 </tests> 94 </tests>
58 95
59 <help><![CDATA[ 96 <help><![CDATA[
60 ============================================================= 97 =============================================================