Mercurial > repos > ebi-gxa > scanpy_plot_embed
comparison scanpy-plot-embedding.xml @ 4:109cfa259d8b draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 400799f99ee36ad12b990b1ccabf4be16a26c003
author | ebi-gxa |
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date | Mon, 25 Nov 2019 14:40:15 -0500 |
parents | b2410da4e381 |
children | 49fe4e682059 |
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3:b2410da4e381 | 4:109cfa259d8b |
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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@+galaxy1"> | 2 <tool id="scanpy_plot_embed" name="Scanpy PlotEmbed" version="@TOOL_VERSION@+galaxy6"> |
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"/> |
15 --legend-loc '${legend_loc}' | 15 --legend-loc '${legend_loc}' |
16 --legend-fontsize '${legend_fontsize}' | 16 --legend-fontsize '${legend_fontsize}' |
17 #if $point_size | 17 #if $point_size |
18 --size ${point_size} | 18 --size ${point_size} |
19 #end if | 19 #end if |
20 #if $gene_symbols_field | |
21 --gene-symbols ${gene_symbols_field} | |
22 #end if | |
20 @PLOT_OPTS@ | 23 @PLOT_OPTS@ |
21 ]]></command> | 24 ]]></command> |
22 | 25 |
23 <inputs> | 26 <inputs> |
24 <expand macro="input_object_params"/> | 27 <expand macro="input_object_params"/> |
26 <param name="color_by" argument="--color" type="text" label="Color by attributes, comma separated texts"> | 29 <param name="color_by" argument="--color" type="text" label="Color by attributes, comma separated texts"> |
27 <sanitizer> | 30 <sanitizer> |
28 <valid initial="string.printable"/> | 31 <valid initial="string.printable"/> |
29 </sanitizer> | 32 </sanitizer> |
30 </param> | 33 </param> |
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'"/> | |
31 <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/> | 35 <param name="use_raw" argument="--use-raw" type="boolean" checked="true" truevalue="--use-raw" falsevalue="--no-raw" label="Use raw attributes if present"/> |
32 <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend"> | 36 <param name="legend_loc" argument="--legend-loc" type="select" label="Location of legend"> |
33 <option value="right margin" selected="true">Right margin</option> | 37 <option value="right margin" selected="true">Right margin</option> |
34 <option value="on data">On data</option> | 38 <option value="on data">On data</option> |
35 </param> | 39 </param> |
38 help="Automatically determined if not specified."/> | 42 help="Automatically determined if not specified."/> |
39 <expand macro="output_plot_params"/> | 43 <expand macro="output_plot_params"/> |
40 </inputs> | 44 </inputs> |
41 | 45 |
42 <outputs> | 46 <outputs> |
43 <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: embedding plot"/> | 47 <data name="output_png" format="png" from_work_dir="output.png" label="${tool.name} on ${on_string}: ${basis} embedding plot"/> |
44 </outputs> | 48 </outputs> |
45 | 49 |
46 <tests> | 50 <tests> |
47 <test> | 51 <test> |
48 <param name="input_obj_file" value="find_cluster.h5"/> | 52 <param name="input_obj_file" value="find_cluster.h5"/> |