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comparison scanpy-plot-embedding.xml @ 4:109cfa259d8b 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 400799f99ee36ad12b990b1ccabf4be16a26c003
author ebi-gxa
date Mon, 25 Nov 2019 14:40:15 -0500
parents b2410da4e381
children 49fe4e682059
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3:b2410da4e381 4:109cfa259d8b
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"/>