scanpy_plot: plot.xml annotate

annotate plot.xml @ 20:62acdd96d4a0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9

author	iuc
date	Fri, 18 Oct 2024 10:37:11 +0000
parents	40812a65a78b
children

rev	line source
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1 <tool id="scanpy_plot" name="Scanpy plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2 <macros>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	3 <import>macros.xml</import>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	4 </macros>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	5 <expand macro="bio_tools"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	6 <expand macro="requirements">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	7 <requirement type="package" version="3.9.1">matplotlib</requirement>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	8 <requirement type="package" version="0.13.2">seaborn</requirement>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	9 <requirement type="package" version="0.11.6">python-igraph</requirement>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	10 </expand>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	11 <stdio>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	12 <regex match="... storing" source="stderr" level="warning"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	13 </stdio>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	14 <expand macro="version_command"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	15 <command detect_errors="exit_code"><![CDATA[
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	16 @CMD@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	17 ]]></command>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	18 <configfiles>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	19 <configfile name="script_file"><![CDATA[
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	20 @CMD_IMPORTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	21 @CMD_READ_INPUTS@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	22
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	23 sc.settings.figdir = '.'
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	24
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	25 #if str($method.method) == 'pl.scatter':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	26
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	27 #if str($method.type.type) == 'xy':
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	28 x_field='$method.type.x'
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	29 y_field='$method.type.y'
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	30
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	31 #if $method.type.log:
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	32 if x_field in adata.obs or x_field in adata.var:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	33 if x_field in adata.obs:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	34 adata.obs[f"log_{x_field}"] = np.log10(adata.obs[x_field])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	35 elif x_field in adata.var:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	36 adata.var[f"log_{x_field}"] = np.log10(adata.var[x_field])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	37 x_field=f"log_{x_field}"
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	38
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	39 if y_field in adata.obs or y_field in adata.var:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	40 if y_field in adata.obs:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	41 adata.obs[f"log_{y_field}"] = np.log10(adata.obs[y_field])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	42 elif y_field in adata.var:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	43 adata.var[f"log_{y_field}"] = np.log10(adata.var[y_field])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	44 y_field=f"log_{y_field}"
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	45 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	46 #end if
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	47
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	48 sc.pl.scatter(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	49 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	50 #if str($method.type.type) == 'xy':
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	51 x=x_field,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	52 y=y_field,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	53 #if str($method.type.color) != '':
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	54 color='$method.type.color',
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	55 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	56 #if str('$method.type.layers.use_layers') == 'true':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	57 layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	58 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	59 #else if str($method.type.type) == 'basis':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	60 basis='$method.type.basis',
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	61 #if str($method.type.color) != '':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	62 #set $color = ([x.strip() for x in str($method.type.color).split(',')])
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	63 color=$color,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	64 #end if
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	65 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	66 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	67 sort_order=$method.sort_order,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	68 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	69 @CMD_PARAM_PL_COMPONENTS@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	70 projection='$method.plot.projection',
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	71 #if str($method.plot.legend_loc) != '':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	72 legend_loc='$method.plot.legend_loc',
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	73 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	74 @CMD_PARAM_LEGEND_FONTSIZE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	75 legend_fontweight='$method.plot.legend_fontweight',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	76 #if $method.plot.color_map:
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	77 color_map='$method.plot.color_map',
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	78 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	79 #if $method.plot.palette:
8 6adf98e782f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec" iuc parents: 7 diff changeset	80 palette=['$method.plot.palette'],
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	81 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	82 frameon=$method.plot.frameon,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	83 @CMD_PARAM_SIZE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	84 @CMD_PARAM_TITLE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	85 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	86
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	87 #else if str($method.method) == 'pl.heatmap':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	88 @CMD_VAR_NAMES_HEADER_CHECK@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	89 sc.pl.heatmap(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	90 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	91 @CMD_PARAMS_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	92 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	93 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	94 @CMD_PARAMS_PL_HEATMAP@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	95 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	96
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	97 #else if str($method.method) == 'pl.dotplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	98 @CMD_VAR_NAMES_HEADER_CHECK@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	99 sc.pl.dotplot(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	100 @CMD_PARAM_PLOT_INPUTS@
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	101 @CMD_PARAMS_INPUTS@
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	102 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	103 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	104 @CMD_PL_DOTPLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	105 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	106
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	107 #else if str($method.method) == 'pl.tracksplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	108 @CMD_VAR_NAMES_HEADER_CHECK@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	109 sc.pl.tracksplot(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	110 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	111 @CMD_PARAMS_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	112 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	113 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	114 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	115
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	116 #else if str($method.method) == 'pl.violin':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	117 sc.pl.violin(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	118 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	119 #if str($method.key_variables.type) == 'var_names':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	120 #set $key_list = adata.var_names
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	121 #else if str($method.key_variables.type) == 'obs':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	122 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	123 #else if str($method.key_variables.type) == 'custom':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	124 #set $key_list=([x.strip() for x in str($method.key_variables.keys).split(',')])
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	125 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	126 keys=$key_list,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	127 #if str($method.groupby) != '':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	128 groupby='$method.groupby',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	129 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	130 log=$method.log,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	131 use_raw=$method.use_raw,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	132 @CMD_CONDITIONAL_STRIPPLOT@
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	133 multi_panel=$method.violin_plot.multi_panel.multi_panel,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	134 ##if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	135 ##figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height),
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	136 ##end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	137 #if str($method.xlabel) != '':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	138 xlabel='$method.xlabel',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	139 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	140 #if str($method.rotation) != '':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	141 rotation=$method.rotation,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	142 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	143 @CMD_PARAMS_SEABORN_VIOLINPLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	144 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	145 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	146
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	147 #else if str($method.method) == 'pl.stacked_violin':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	148 @CMD_VAR_NAMES_HEADER_CHECK@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	149 sc.pl.stacked_violin(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	150 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	151 @CMD_PARAMS_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	152 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	153 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	154 @CMD_PARAMS_PL_STACKED_VIOLIN@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	155 @CMD_SHOW_NONE@)
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	156
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	157 #else if str($method.method) == 'pl.matrixplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	158 @CMD_VAR_NAMES_HEADER_CHECK@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	159 sc.pl.matrixplot(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	160 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	161 @CMD_PARAMS_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	162 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	163 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	164 @CMD_PARAMS_PL_MATRIXPLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	165 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	166
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	167 #else if str($method.method) == 'pl.clustermap':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	168 sc.pl.clustermap(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	169 #if str($method.use_raw) == 'True':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	170 adata=adata.X,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	171 #else
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	172 adata=adata,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	173 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	174 #if str($method.obs_keys) != '':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	175 obs_keys='$method.obs_keys',
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	176 #end if
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	177 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	178 method='$method.seaborn_clustermap.method',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	179 metric='$method.seaborn_clustermap.metric',
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	180 #if str($method.seaborn_clustermap.z_score) != 'None':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	181 z_score=$method.seaborn_clustermap.z_score,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	182 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	183 #if str($method.seaborn_clustermap.standard_scale) != 'None':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	184 standard_scale=$method.seaborn_clustermap.standard_scale,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	185 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	186 col_cluster=$method.seaborn_clustermap.col_cluster,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	187 row_cluster=$method.seaborn_clustermap.row_cluster,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	188 save='.$format',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	189 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	190
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	191 #else if str($method.method) == 'pl.highest_expr_genes':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	192 sc.pl.highest_expr_genes(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	193 @CMD_PARAM_PLOT_INPUTS@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	194 n_top=$method.n_top,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	195 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	196 #if str($method.setseaborn_boxplot.color) != '':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	197 color='$method.setseaborn_boxplot.color',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	198 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	199 #if $method.setseaborn_boxplot.palette:
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	200 palette='$method.setseaborn_boxplot.palette',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	201 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	202 saturation=$method.setseaborn_boxplot.saturation,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	203 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	204
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	205 #else if str($method.method) == 'pl.highly_variable_genes':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	206 sc.pl.highly_variable_genes(
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	207 adata_or_result=adata,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	208 log=$method.log,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	209 save='.$format',
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	210 highly_variable_genes=$method.highly_variable_genes,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	211 @CMD_SHOW_NONE@)
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	212
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	213 #else if str($method.method) == 'pl.scrublet_score_distribution':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	214 sc.pl.scrublet_score_distribution(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	215 adata=adata,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	216 scale_hist_obs='$method.scale_hist_obs',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	217 scale_hist_sim='$method.scale_hist_sim',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	218 @CMD_PARAMS_FIGSIZE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	219 save='.$format',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	220 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	221
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	222 #else if str($method.method) == 'pl.pca':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	223 sc.pl.pca(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	224 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	225 @CMD_PARAM_COLOR@
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	226 @CMD_PARAM_GENE_SYMBOLS@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	227 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	228 sort_order=$method.sort_order,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	229 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	230 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	231 @CMD_SCATTER_OUTINE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	232 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	233 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	234 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	235
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	236 #else if str($method.method) == 'pl.pca_loadings':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	237 sc.pl.pca_loadings(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	238 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	239 #set $components = ([int(x.strip()) for x in str($method.components).split(',')])
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	240 components=$components,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	241 include_lowest=$method.include_lowest,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	242 #if str($method.n_points) != '':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	243 n_points=$method.n_points,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	244 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	245 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	246
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	247 #else if str($method.method) == 'pl.pca_variance_ratio':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	248 sc.pl.pca_variance_ratio(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	249 @CMD_PARAM_PLOT_INPUTS@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	250 n_pcs=$method.n_pcs,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	251 log=$method.log,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	252 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	253
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	254 #else if str($method.method) == 'pl.pca_overview':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	255 sc.pl.pca_overview(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	256 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	257 @CMD_PARAM_COLOR@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	258 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	259 sort_order=$method.sort_order,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	260 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	261 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	262 @CMD_SCATTER_OUTINE@
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	263 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	264 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	265
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	266 #else if str($method.method) == 'pl.tsne':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	267 sc.pl.tsne(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	268 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	269 @CMD_PARAM_COLOR@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	270 @CMD_PARAM_GENE_SYMBOLS@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	271 use_raw=$method.use_raw,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	272 @CMD_PL_EDGES@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	273 arrows=$method.arrows,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	274 sort_order=$method.sort_order,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	275 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	276 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	277 @CMD_SCATTER_OUTINE@
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	278 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	279 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	280 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	281
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	282 #else if str($method.method) == 'pl.umap':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	283 sc.pl.umap(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	284 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	285 @CMD_PARAM_COLOR@
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	286 @CMD_PARAM_GENE_SYMBOLS@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	287 use_raw=$method.use_raw,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	288 @CMD_PL_EDGES@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	289 arrows=$method.arrows,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	290 sort_order=$method.sort_order,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	291 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	292 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	293 @CMD_SCATTER_OUTINE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	294 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	295 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	296 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	297
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	298 #else if str($method.method) == 'pl.diffmap':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	299 sc.pl.diffmap(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	300 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	301 @CMD_PARAM_COLOR@
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	302 @CMD_PARAM_GENE_SYMBOLS@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	303 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	304 sort_order=$method.sort_order,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	305 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	306 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	307 @CMD_SCATTER_OUTINE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	308 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	309 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	310 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	311
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	312 #else if str($method.method) == 'pl.draw_graph':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	313 sc.pl.draw_graph(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	314 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	315 @CMD_PARAM_COLOR@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	316 @CMD_PARAM_GENE_SYMBOLS@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	317 use_raw=$method.use_raw,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	318 layout='$method.layout',
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	319 @CMD_PL_EDGES@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	320 arrows=$method.arrows,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	321 sort_order=$method.sort_order,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	322 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	323 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	324 @CMD_SCATTER_OUTINE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	325 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	326 @CMD_PARAM_LAYER@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	327 @CMD_SHOW_NONE@)
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	328
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	329 #else if str($method.method) == 'pl.embedding_density':
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	330 sc.pl.embedding_density(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	331 @CMD_PARAM_PLOT_INPUTS@
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	332 basis='$method.basis',
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	333 #if str($method.key) != '':
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	334 key='$method.key',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	335 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	336 #if str($method.groupby) != '':
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	337 groupby='$method.groupby',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	338 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	339 #if str($method.group) != '':
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	340 #set $group = ([x.strip() for x in str($method.group).split(',')])
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	341 group=$group,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	342 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	343 #if $method.color_map:
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	344 color_map='$method.color_map',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	345 #end if
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	346 bg_dotsize=$method.bg_dotsize,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	347 fg_dotsize=$method.fg_dotsize,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	348 ncols=$method.ncols,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	349 wspace=$method.wspace,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	350 hspace=$method.hspace,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	351 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	352
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	353
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	354
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	355 #else if str($method.method) == 'pl.dpt_timeseries':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	356 sc.pl.dpt_timeseries(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	357 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	358 #if str($method.heatmap.as_heatmap) == 'True'
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	359 #if $method.heatmap.color_map
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	360 color_map='$method.heatmap.color_map',
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	361 #end if
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	362 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	363 as_heatmap=$method.heatmap.as_heatmap,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	364 @CMD_SHOW_NONE@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	365
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	366 #else if str($method.method) == 'pl.paga':
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	367 sc.pl.paga(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	368 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	369 @CMD_PARAMS_PL_PAGA@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	370 @CMD_SHOW_NONE@)
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	371
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	372 @CMD_ANNDATA_WRITE_OUTPUTS@
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	373
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	374 #else if str($method.method) == 'pl.paga_compare':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	375 sc.pl.paga_compare(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	376 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	377 @CMD_PARAMS_PL_PAGA@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	378 @CMD_PARAM_PL_COMPONENTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	379 projection='$method.plot.projection',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	380 #if str($method.plot.legend_loc) != '':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	381 legend_loc='$method.plot.legend_loc',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	382 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	383 @CMD_PARAM_LEGEND_FONTSIZE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	384 legend_fontweight='$method.plot.legend_fontweight',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	385 #if $method.plot.color_map:
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	386 color_map='$method.plot.color_map',
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	387 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	388 #if $method.plot.palette:
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	389 palette=['$method.plot.palette'],
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	390 #end if
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	391 @CMD_PARAM_SIZE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	392 @CMD_PARAM_TITLE@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	393 @CMD_SHOW_NONE@)
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	394
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	395 #else if str($method.method) == 'pl.paga_path':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	396 sc.pl.paga_path(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	397 @CMD_PARAM_PLOT_INPUTS@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	398 #set $nodes = ([int(x.strip()) for x in str($method.nodes).split(',')])
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	399 nodes=$nodes,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	400 #set $keys=([x.strip() for x in str($method.keys).split(',')])
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	401 keys=$keys,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	402 use_raw=$method.use_raw,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	403 #if str($method.annotations) != '':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	404 #set $annotations=([x.strip() for x in str($method.annotations).split(',')])
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	405 annotations=$annotations,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	406 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	407 #if $method.color_map:
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	408 color_map='$method.color_map',
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	409 #end if
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	410 n_avg=$method.n_avg,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	411 #if str($method.annotations) != '':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	412 groups_key='$method.groups_key',
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	413 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	414 as_heatmap=$method.as_heatmap,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	415 show_node_names=$method.show_node_names,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	416 show_colorbar=$method.show_colorbar,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	417 show_yticks=$method.show_yticks,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	418 normalize_to_zero_one=$method.normalize_to_zero_one,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	419 @CMD_SHOW_NONE@)
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	420
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	421 #else if str($method.method) == 'pl.rank_genes_groups':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	422 sc.pl.rank_genes_groups(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	423 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	424 @CMD_PARAM_GROUPS@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	425 n_genes=$method.n_genes,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	426 @CMD_PARAM_GENE_SYMBOLS@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	427 fontsize=$method.fontsize,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	428 ncols=$method.ncols,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	429 sharey=$method.sharey,
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	430 @CMD_SHOW_NONE@)
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	431
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	432 #else if $method.method == 'pl.rank_genes_groups_violin'
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	433 sc.pl.rank_genes_groups_violin(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	434 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	435 @CMD_PARAM_GROUPS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	436 #if str($method.genes.select) == 'n_genes':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	437 n_genes=$method.genes.n_genes,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	438 #else
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	439 #set $gene_names = ([x.strip() for x in str($method.genes.gene_names).split(',')])
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	440 gene_names=$gene_names,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	441 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	442 @CMD_PARAM_GENE_SYMBOLS@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	443 use_raw=$method.use_raw,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	444 split=$method.split,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	445 strip=$method.violin_plot.stripplot.stripplot,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	446 #if str($method.violin_plot.stripplot.stripplot) == 'True':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	447 jitter=$method.violin_plot.stripplot.jitter.jitter,
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	448 #if str($method.violin_plot.stripplot.jitter.jitter) == 'True':
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	449 size=$method.violin_plot.stripplot.jitter.size,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	450 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	451 #end if
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	452 density_norm='$method.violin_plot.density_norm',
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	453 @CMD_SHOW_NONE@)
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	454
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	455 #else if str($method.method) == 'pl.rank_genes_groups_stacked_violin':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	456 @CMD_VAR_NAMES_HEADER_CHECK@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	457 sc.pl.rank_genes_groups_stacked_violin(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	458 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	459 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	460 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	461 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	462 @CMD_PARAMS_PL_STACKED_VIOLIN@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	463 @CMD_SHOW_NONE@)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	464
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	465 #else if str($method.method) == 'pl.rank_genes_groups_heatmap':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	466 @CMD_VAR_NAMES_HEADER_CHECK@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	467 sc.pl.rank_genes_groups_heatmap(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	468 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	469 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	470 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	471 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	472 @CMD_PARAMS_PL_HEATMAP@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	473 @CMD_SHOW_NONE@)
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	474
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	475 #else if str($method.method) == 'pl.rank_genes_groups_dotplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	476 @CMD_VAR_NAMES_HEADER_CHECK@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	477 sc.pl.rank_genes_groups_dotplot(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	478 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	479 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	480 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	481 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	482 @CMD_PL_DOTPLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	483 @CMD_VALUES_TO_PLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	484 @CMD_SHOW_NONE@)
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	485
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	486 #else if str($method.method) == 'pl.rank_genes_groups_matrixplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	487 @CMD_VAR_NAMES_HEADER_CHECK@
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	488 sc.pl.rank_genes_groups_matrixplot(
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	489 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	490 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	491 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	492 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	493 @CMD_PARAMS_PL_MATRIXPLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	494 @CMD_VALUES_TO_PLOT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	495 @CMD_SHOW_NONE@)
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	496
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	497 #else if str($method.method) == 'pl.rank_genes_groups_tracksplot':
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	498 @CMD_VAR_NAMES_HEADER_CHECK@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	499 sc.pl.rank_genes_groups_tracksplot(
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	500 @CMD_PARAM_PLOT_INPUTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	501 @CMD_PL_RANK_GENES_GROUPS_EXT@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	502 @CMD_PARAMS_PLOTS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	503 @CMD_PARAM_GENE_SYMBOLS@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	504 @CMD_PARAMS_PL_HEATMAP@
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	505 @CMD_SHOW_NONE@)
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	506
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	507 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	508 ]]></configfile>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	509 </configfiles>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	510 <inputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	511 <expand macro="inputs_anndata"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	512 <expand macro="param_plot_format"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	513 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	514 <param argument="method" type="select" label="Method used for plotting">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	515 <option value="pl.scatter">Generic: Scatter plot along observations or variables axes, using 'pl.scatter'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	516 <option value="pl.heatmap">Generic: Heatmap of the expression values of set of genes, using 'pl.heatmap'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	517 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using 'pl.dotplot'</option>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	518 <option value="pl.tracksplot">Generic: Makes a tracks plot of the expression values per cell, using 'pl.tracksplot'</option>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	519 <option value="pl.violin">Generic: Violin plot, using 'pl.violin'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	520 <option value="pl.stacked_violin">Generic: Stacked violin plots, using 'pl.stacked_violin'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	521 <option value="pl.matrixplot">Generic: Heatmap of the mean expression values per cluster, using 'pl.matrixplot'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	522 <option value="pl.clustermap">Generic: Hierarchically-clustered heatmap, using 'pl.clustermap'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	523 <option value="pl.highest_expr_genes">Preprocessing: Plot the fraction of counts assigned to each gene over all cells, using 'pl.highest_expr_genes'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	524 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using 'pl.highly_variable_genes'</option>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	525 <option value="pl.scrublet_score_distribution">Preprocessing: Plot histogram of doublet scores, using 'pl.scrublet_score_distribution'</option>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	526 <option value="pl.pca">PCA: Scatter plot in PCA coordinates, using 'pl.pca'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	527 <option value="pl.pca_loadings">PCA: Rank genes according to contributions to PCs, using 'pl.pca_loadings'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	528 <option value="pl.pca_variance_ratio">PCA: Scatter plot in PCA coordinates, using 'pl.pca_variance_ratio'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	529 <option value="pl.pca_overview">PCA: Plot PCA results, using 'pl.pca_overview'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	530 <option value="pl.tsne">Embeddings: Scatter plot in tSNE basis, using 'pl.tsne'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	531 <option value="pl.umap">Embeddings: Scatter plot in UMAP basis, using 'pl.umap'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	532 <option value="pl.diffmap">Embeddings: Scatter plot in Diffusion Map basis, using 'pl.diffmap'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	533 <option value="pl.draw_graph">Embeddings: Scatter plot in graph-drawing basis, using 'pl.draw_graph'</option>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	534 <option value="pl.embedding_density">Embeddings: Plot the density of cells in an embedding (per condition), using 'pl.embedding_density'</option>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	535 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	536 <!-- <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option> -->
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	537 <option value="pl.dpt_timeseries">Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series, using 'pl.dpt_timeseries'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	538 <option value="pl.paga">Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges, using 'pl.paga'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	539 <option value="pl.paga_compare">Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side, using 'pl.paga_compare'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	540 <option value="pl.paga_path">Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths, using 'pl.paga_path'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	541 <option value="pl.rank_genes_groups">Marker genes: Plot ranking of genes using dotplot plot, using 'pl.rank_genes_groups'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	542 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	543 <option value="pl.rank_genes_groups_stacked_violin">Marker genes: Plot ranking of genes as stacked violin plot, using 'pl.rank_genes_groups_stacked_violin'</option>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	544 <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	545 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	546 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	547 <option value="pl.rank_genes_groups_tracksplot">Marker genes: Plot ranking of genes as tracksplot plot, using 'pl.rank_genes_groups_tracksplot'</option>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	548 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	549 <when value="pl.scatter">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	550 <conditional name="type">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	551 <param name="type" type="select" label="Plotting tool that computed coordinates">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	552 <option value="xy" selected="true">Using coordinates</option>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	553 <option value="basis">Using tool that computes coordinates</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	554 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	555 <when value="xy">
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	556 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	557 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	558 </param>
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	559 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	560 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	561 </param>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	562 <expand macro="param_log"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	563 <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	564 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	565 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	566 <conditional name="layers">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	567 <param argument="use_layers" type="select" label="Use the layers attribute?">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	568 <option value="false" selected="true">No</option>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	569 <option value="true">Yes</option>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	570 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	571 <when value="true">
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	572 <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	573 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	574 </param>
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	575 <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	576 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	577 </param>
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	578 <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	579 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	580 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	581 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	582 <when value="false"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	583 </conditional>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	584 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	585 <when value="basis">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	586 <param argument="basis" type="select" label="Plotting tool that computes coordinates">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	587 <option value="pca">pca (need to run on 'pl.pca' output)</option>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	588 <option value="tsne">tsne (need to run on 'tl.tsne' output)</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	589 <option value="umap">umap (need to run on 'tl.umap' output)</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	590 <option value="diffmap">diffmap (need to run on 'tl.diffmap' output)</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	591 <option value="draw_graph_fr">draw_graph_fr (need to run on 'tl.draw_graph' output)</option>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	592 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	593 <expand macro="param_color"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	594 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	595 </conditional>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	596 <expand macro="param_use_raw" falsevalue="None"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	597 <param argument="sort_order" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot data points with higher values on top of others?" help="For continuous annotations used as color parameter"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	598 <expand macro="param_groups"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	599 <section name="plot" title="Plot attributes">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	600 <expand macro="param_pl_components"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	601 <expand macro="param_projection"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	602 <expand macro="param_legend_loc"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	603 <expand macro="param_legend_fontsize"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	604 <expand macro="param_legend_fontweight"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	605 <expand macro="param_color_map"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	606 <expand macro="param_palette"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	607 <expand macro="param_frameon"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	608 <expand macro="param_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	609 <expand macro="param_title"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	610 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	611 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	612 <when value="pl.heatmap">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	613 <expand macro="params_inputs"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	614 <expand macro="param_gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	615 <expand macro="params_plots"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	616 <expand macro="params_pl_heatmap"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	617 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	618 <when value="pl.dotplot">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	619 <expand macro="params_inputs"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	620 <expand macro="param_gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	621 <expand macro="params_plots"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	622 <expand macro="params_pl_dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	623 </when>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	624 <when value="pl.tracksplot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	625 <expand macro="params_inputs"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	626 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	627 <expand macro="params_plots"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	628 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	629 <when value="pl.violin">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	630 <conditional name="key_variables">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	631 <param name="type" type="select" label="Keys for accessing variables">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	632 <option value="var_names" selected="true">All variables in '.var_names'</option>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	633 <option value="obs">All fields in '.obs'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	634 <option value="custom">Subset of variables in 'adata.var_names' or fields of '.obs'</option>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	635 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	636 <when value="var_names"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	637 <when value="obs"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	638 <when value="custom">
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	639 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	640 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	641 </param>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	642 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	643 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	644 <expand macro="param_groupby"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	645 <expand macro="param_log"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	646 <expand macro="param_use_raw" falsevalue="None"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	647 <section name="violin_plot" title="Violin plot attributes">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	648 <expand macro="conditional_stripplot"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	649 <conditional name="multi_panel">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	650 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when 'groupby is not provided">
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	651 <option value="None" selected="true">No</option>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	652 <option value="True">Yes</option>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	653 </param>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	654 <when value="None"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	655 <when value="True">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	656 <!-- <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	657 <param argument="height" type="integer" min="0" value="" optional="true" label="Height of the figure"/> -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	658 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	659 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	660 </section>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	661 <param argument="xlabel" type="text" value="" optional="true" label="Label of the x axis" help="Defaults to 'groupby' if 'rotation' is 'None', otherwise, no label is shown.">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	662 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	663 </param>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	664 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	665 <expand macro="params_seaborn_violinplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	666 <expand macro="param_layer"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	667 </when>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	668 <when value="pl.stacked_violin">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	669 <expand macro="params_inputs"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	670 <expand macro="param_gene_symbols"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	671 <expand macro="params_plots"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	672 <expand macro="params_pl_stacked_violin"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	673 </when>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	674 <when value="pl.matrixplot">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	675 <expand macro="params_inputs"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	676 <expand macro="param_gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	677 <expand macro="params_plots"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	678 <expand macro="params_pl_matrixplot"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	679 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	680 <when value="pl.clustermap">
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	681 <param argument="obs_keys" type="text" value="" optional="true" label="Categorical annotation to plot with a different color map" help="Currently, only a single key is supported.">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	682 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	683 </param>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	684 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	685 <section name="seaborn_clustermap" title="Parameters for seaborn.clustermap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	686 <param name="method" type="select" label="Linkage method to use for calculating clusters" help="More details in https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	687 <option value="average" selected="true">average: UPGMA algorithm</option>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	688 <option value="single">single: Nearest Point Algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	689 <option value="complete">complete: Farthest Point Algorithm or Voor Hees Algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	690 <option value="weighted">weighted: WPGMA algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	691 <option value="centroid">centroid: UPGMC algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	692 <option value="median">median: WPGMC algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	693 <option value="ward">ward: incremental algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	694 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	695 <param name="metric" type="select" label="Distance metric to use for the data" help="See scipy.spatial.distance.pdist documentation for more options https://docs.scipy.org/doc/scipy/reference/generated/scipy.spatial.distance.pdist.html">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	696 <expand macro="distance_metric_options"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	697 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	698 <param name="z_score" type="select" label="Calculate z-scores for the rows or the columns?" help="Z scores are: z = (x - mean)/std, so values in each row (column) will get the mean of the row (column) subtracted, then divided by the standard deviation of the row (column). This ensures that each row (column) has mean of 0 and variance of 1.">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	699 <option value="None" selected="true">No Z-score</option>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	700 <option value="0">Rows</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	701 <option value="1">Columns</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	702 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	703 <param name="standard_scale" type="select" label="Standardize a dimension?" help="It means for each row or column, subtract the minimum and divide each by its maximum.">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	704 <option value="None" selected="true">No standardization</option>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	705 <option value="0">Rows</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	706 <option value="1">Columns</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	707 </param>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	708 <param name="col_cluster" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Cluster the columns?"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	709 <param name="row_cluster" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Cluster the rows?"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	710 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	711 </when>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	712 <when value="pl.highest_expr_genes">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	713 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	714 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	715 <expand macro="param_log"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	716 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	717 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	718 <expand macro="sanitize_query"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	719 </param>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	720 <param argument="palette" type="select" optional="true" label="Colors to use for the different levels of the hue variable" help="See https://seaborn.pydata.org/tutorial/color_palettes.html for more details.">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	721 <expand macro="seaborn_color_palette_options"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	722 </param>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	723 <param argument="saturation" type="float" value="0.75" label="Proportion of the original saturation to draw colors at" help="Large patches often look better with slightly desaturated colors, but set this to 1 if you want the plot colors to perfectly match the input color spec."/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	724 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	725 </when>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	726 <when value="pl.highly_variable_genes">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	727 <expand macro="param_log"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	728 <param argument="highly_variable_genes" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot highly variable genes or gene subset?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	729 </when>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	730 <when value="pl.scrublet_score_distribution">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	731 <param name="scale_hist_obs" type="select" label="Set y axis scale transformation in matplotlib for the plot of observed transcriptomes">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	732 <option value="log" selected="true">log</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	733 <option value="linear">linear</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	734 <option value="symlog">symlog</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	735 <option value="logit">logit</option>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	736 </param>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	737 <param name="scale_hist_sim" type="select" label="Set y axis scale transformation in matplotlib for the plot of simulated doublets">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	738 <option value="linear" selected="true">linear</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	739 <option value="log">log</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	740 <option value="symlog">symlog</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	741 <option value="logit">logit</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	742 </param>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	743 <expand macro="pl_figsize"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	744 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	745 <when value="pl.pca">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	746 <expand macro="param_color"/>
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	747 <expand macro="param_gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	748 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	749 <expand macro="param_sort_order"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	750 <expand macro="param_groups"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	751 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	752 <expand macro="params_scatter_outine"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	753 <expand macro="section_matplotlib_pyplot_scatter"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	754 <expand macro="param_layer"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	755 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	756 <when value="pl.pca_loadings">
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	757 <param argument="components" type="text" value="1,2,3" label="List of comma-separated components" help="1, 2, 3 means first, second and third principal components">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	758 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	759 </param>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	760 <param argument="include_lowest" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the variables with both highest and lowest loadings"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	761 <param argument="n_points" type="integer" value="" optional="true" label="Number of variables to plot for each component"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	762 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	763 <when value="pl.pca_variance_ratio">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	764 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	765 <expand macro="param_log"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	766 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	767 <when value="pl.pca_overview">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	768 <expand macro="param_color"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	769 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	770 <expand macro="param_sort_order"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	771 <expand macro="param_groups"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	772 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	773 <expand macro="params_scatter_outine"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	774 <expand macro="section_matplotlib_pyplot_scatter"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	775 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	776 <when value="pl.tsne">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	777 <expand macro="param_color"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	778 <expand macro="param_gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	779 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	780 <expand macro="pl_edges"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	781 <expand macro="param_arrows"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	782 <expand macro="param_sort_order"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	783 <expand macro="param_groups"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	784 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	785 <expand macro="params_scatter_outine"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	786 <expand macro="section_matplotlib_pyplot_scatter"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	787 <expand macro="param_layer"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	788 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	789 <when value="pl.umap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	790 <expand macro="param_color"/>
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	791 <expand macro="param_gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	792 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	793 <expand macro="pl_edges"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	794 <expand macro="param_arrows"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	795 <expand macro="param_sort_order"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	796 <expand macro="param_groups"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	797 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	798 <expand macro="params_scatter_outine"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	799 <expand macro="section_matplotlib_pyplot_scatter"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	800 <expand macro="param_layer"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	801 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	802 <when value="pl.diffmap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	803 <expand macro="param_color"/>
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	804 <expand macro="param_gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	805 <expand macro="param_use_raw"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	806 <expand macro="param_sort_order"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	807 <expand macro="param_groups"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	808 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	809 <expand macro="params_scatter_outine"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	810 <expand macro="section_matplotlib_pyplot_scatter"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	811 <expand macro="param_layer"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	812 </when>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	813 <when value="pl.draw_graph">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	814 <expand macro="param_color"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	815 <expand macro="param_gene_symbols"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	816 <expand macro="param_use_raw"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	817 <param argument="layout" type="select" optional="false" label="Plotting layout">
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	818 <expand macro="options_layout"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	819 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	820 <expand macro="pl_edges"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	821 <expand macro="param_arrows"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	822 <expand macro="param_sort_order"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	823 <expand macro="param_groups"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	824 <expand macro="params_pl_attribute_section"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	825 <expand macro="params_scatter_outine"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	826 <expand macro="section_matplotlib_pyplot_scatter"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	827 <expand macro="param_layer"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	828 </when>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	829 <when value="pl.embedding_density">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	830 <param argument="basis" type="text" value="umap" label="The embedding over which the density was calculated." help="This embedded representation should be found in adata.obsm['X_[basis]']">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	831 <expand macro="sanitize_query"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	832 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	833 <param argument="key" type="text" optional="true" value="" label="Name of the .obs covariate that contains the density estimates" help="Alternatively, pass _groupby_.">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	834 <expand macro="sanitize_query"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	835 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	836 <param argument="groupby" type="text" optional="true" value="" label="Name of the condition used in tl.embedding_density" help="Alternatively, pass _key_.">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	837 <expand macro="sanitize_query"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	838 </param>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	839 <param argument="group" type="text" optional="all" value="" label="The category in the categorical observation annotation to be plotted"
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	840 help="For example, 'G1' in the cell cycle 'phase' covariate. If multiple categories want to be plotted use a comma separated list">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	841 <expand macro="sanitize_query"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	842 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	843 <expand macro="param_color_map"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	844 <param argument="bg_dotsize" type="integer" min="0" value="80" label="Dot size for background data points not in the group"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	845 <param argument="fg_dotsize" type="integer" min="0" value="180" label="Dot size for foreground data points in the group"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	846 <expand macro="param_ncols"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	847 <expand macro="param_wspace"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	848 <expand macro="param_hspace"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	849 </when>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	850 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	851 <!-- <when value="pl.dpt_groups_pseudotime">
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	852 <expand macro="param_color_map"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	853 </when> -->
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	854 <when value="pl.dpt_timeseries">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	855 <conditional name="heatmap">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	856 <param argument="as_heatmap" type="select" label="Plot the timeseries as heatmap?">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	857 <option value="True" selected="true">Yes</option>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	858 <option value="False">No</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	859 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	860 <when value="True">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	861 <expand macro="param_color_map"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	862 </when>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	863 <when value="False"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	864 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	865 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	866 <when value="pl.paga">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	867 <expand macro="params_pl_paga"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	868 </when>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	869 <when value="pl.paga_compare">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	870 <expand macro="params_pl_paga"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	871 <section name="plot" title="Plot attributes">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	872 <expand macro="param_pl_components"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	873 <expand macro="param_projection"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	874 <expand macro="param_legend_loc">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	875 <option value="on data">on data</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	876 <option value="right margin">right margin</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	877 </expand>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	878 <expand macro="param_legend_fontsize"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	879 <expand macro="param_legend_fontweight"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	880 <expand macro="param_color_map"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	881 <expand macro="param_palette"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	882 <expand macro="param_frameon"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	883 <expand macro="param_size"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	884 <expand macro="param_title"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	885 </section>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	886 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	887 <when value="pl.paga_path">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	888 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph" help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	889 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	890 </param>
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	891 <param argument="keys" type="text" value="" label="Keys for accessing variables" help="One or a list of comma-separated index or key from '.var_names' or fields of '.obs'">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	892 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	893 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	894 <expand macro="param_use_raw"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	895 <param argument="annotations" type="text" value="dpt_pseudotime" optional="true" label="Key to plot" help="Keys for obs, comma-separated">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	896 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	897 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	898 <expand macro="param_color_map"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	899 <param argument="n_avg" type="integer" value="1" label="Number of data points to include in computation of running average"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	900 <param argument="groups_key" type="text" value="" optional="true" label="Key of the grouping used to run PAGA" help="If not set, use uns/page/groups">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	901 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	902 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	903 <param argument="as_heatmap" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the timeseries as heatmap?" help="If not, annotations have no effect."/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	904 <param argument="show_node_names" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Plot the node names on the nodes bar?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	905 <param argument="show_colorbar" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the colorbar?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	906 <param argument="show_yticks" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Show the y ticks?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	907 <param argument="normalize_to_zero_one" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Shift and scale the running average to [0, 1] per gene?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	908 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	909 <when value="pl.rank_genes_groups">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	910 <expand macro="param_groups"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	911 <expand macro="param_n_genes" value="20"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	912 <expand macro="param_gene_symbols"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	913 <param argument="fontsize" type="integer" min="0" value="8" label="Font size for gene names"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	914 <expand macro="param_ncols"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	915 <param argument="sharey" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Should the y-axis of each panels be shared?" help="If not, each panel has its own y-axis range"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	916 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	917 <when value="pl.rank_genes_groups_violin">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	918 <expand macro="param_groups"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	919 <conditional name="genes">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	920 <param argument="select" type="select" label="Which genes to plot?">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	921 <option value="n_genes" selected="true">A number of genes</option>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	922 <option value="gene_names">A custom list of genes</option>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	923 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	924 <when value="n_genes">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	925 <expand macro="param_n_genes" value="20"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	926 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	927 <when value="gene_names">
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	928 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	929 <expand macro="sanitize_query"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	930 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	931 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	932 </conditional>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	933 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	934 <expand macro="param_use_raw" falsevalue="None"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	935 <param argument="split" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Split the violins?"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	936 <section name="violin_plot" title="Violin plot attributes">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	937 <expand macro="conditional_stripplot"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	938 <param argument="density_norm" type="select" label="Method used to scale the width of each violin">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	939 <option value="width" selected="true">width: each violin will have the same width</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	940 <option value="area">area: each violin will have the same area</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	941 <option value="count">count: the width of the violins will be scaled by the number of observations in that bin</option>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	942 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	943 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	944 </when>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	945 <when value="pl.rank_genes_groups_stacked_violin">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	946 <expand macro="pl_rank_genes_groups_ext"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	947 <expand macro="params_plots"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	948 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	949 <expand macro="params_pl_stacked_violin"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	950 </when>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	951 <when value="pl.rank_genes_groups_heatmap">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	952 <expand macro="pl_rank_genes_groups_ext"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	953 <expand macro="params_plots"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	954 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	955 <expand macro="params_pl_heatmap"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	956 </when>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	957 <when value="pl.rank_genes_groups_dotplot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	958 <expand macro="pl_rank_genes_groups_ext"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	959 <expand macro="params_plots"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	960 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	961 <expand macro="params_pl_dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	962 <expand macro="values_to_plot"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	963 </when>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	964 <when value="pl.rank_genes_groups_matrixplot">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	965 <expand macro="pl_rank_genes_groups_ext"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	966 <expand macro="params_plots"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	967 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	968 <expand macro="params_pl_matrixplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	969 <expand macro="values_to_plot"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	970 </when>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	971 <when value="pl.rank_genes_groups_tracksplot">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	972 <expand macro="pl_rank_genes_groups_ext"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	973 <expand macro="params_plots"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	974 <expand macro="param_gene_symbols"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	975 <expand macro="params_pl_heatmap"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	976 </when>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	977 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	978 <expand macro="inputs_common_advanced"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	979 </inputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	980 <outputs>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	981 <data name="out_png" format="png" from_work_dir="*.png" label="PNG plot from ${tool.name} (${method.method}) on ${on_string}">
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	982 <filter>format == 'png' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	983 </data>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	984 <collection name="collection_png" type="list" label="PNG plots from ${tool.name} (${method.method}) on ${on_string}">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	985 <discover_datasets pattern="rank_genes_groups_(?P<designation>.*).png" format="png"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	986 <filter>format == 'png' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	987 </collection>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	988 <data name="out_pdf" format="pdf" from_work_dir="*.pdf" label="PDF plot from ${tool.name} (${method.method}) on ${on_string}">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	989 <filter>format == 'pdf' and method['method'] != 'pl.rank_genes_groups_violin'</filter>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	990 </data>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	991 <collection name="collection_pdf" type="list" label="PDF plots from ${tool.name} (${method.method}) on ${on_string}">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	992 <discover_datasets pattern="rank_genes_groups_(?P<designation>.*).pdf" format="pdf"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	993 <filter>format == 'pdf' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	994 </collection>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	995 <data name="out_svg" format="svg" from_work_dir="*.svg" label="SVG plot from ${tool.name} (${method.method}) on ${on_string}">
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	996 <filter>format == 'svg' and method['method'] != pl.rank_genes_groups_violin</filter>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	997 </data>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	998 <collection name="collection_svg" type="list" label="SVG plots from ${tool.name} (${method.method}) on ${on_string}">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	999 <discover_datasets pattern="rank_genes_groups_(?P<designation>.*).svg" format="svg"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1000 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1001 </collection>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1002 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1003 <filter>advanced_common['show_log']</filter>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1004 </data>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1005 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1006 <filter>method['method'] == 'pl.paga'</filter>
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1007 </data>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1008 </outputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1009 <tests>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1010 <!-- test 1 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1011 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1012 <param name="adata" value="pbmc68k_reduced.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1013 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1014 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1015 <param name="method" value="pl.scatter"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1016 <conditional name="type">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1017 <param name="type" value="basis"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1018 <param name="basis" value="umap"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1019 <param name="color" value="HES4"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1020 </conditional>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1021 <param name="use_raw" value="True"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1022 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1023 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1024 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1025 <param name="color_map" value="inferno"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1026 <param name="palette" value="inferno"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1027 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1028 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1029 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1030 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1031 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1032 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1033 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1034 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1035 <has_text_matching expression="sc.pl.scatter"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1036 <has_text_matching expression="basis='umap'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1037 <has_text_matching expression="color=\['HES4'\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1038 <has_text_matching expression="use_raw=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1039 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1040 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1041 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1042 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1043 <has_text_matching expression="color_map='inferno'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1044 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1045 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1046 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1047 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1048 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1049 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1050
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1051 <!-- test 2 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1052 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1053 <param name="adata" value="krumsiek11.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1054 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1055 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1056 <param name="method" value="pl.scatter"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1057 <conditional name="type">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1058 <param name="type" value="xy"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1059 <param name="x" value="EKLF"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1060 <param name="y" value="Cebpa"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1061 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1062 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1063 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1064 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1065 <param name="palette" value="bwr"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1066 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1067 <param name="title" value="A title"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1068 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1069 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1070 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1071 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1072 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1073 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1074 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1075 <has_text_matching expression="sc.pl.scatter"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1076 <has_text_matching expression="x_field='EKLF'"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1077 <has_text_matching expression="y_field='Cebpa'"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1078 <has_text_matching expression="use_raw=None"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1079 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1080 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1081 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1082 <has_text_matching expression="legend_fontweight='normal'"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1083 <has_text_matching expression="frameon=True"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1084 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1085 <has_text_matching expression="title='A title'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1086 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1087 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1088 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1089 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1090
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1091 <!-- test 3 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1092 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1093 <param name="adata" value="pbmc68k_reduced.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1094 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1095 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1096 <param name="method" value="pl.scatter"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1097 <conditional name="type">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1098 <param name="type" value="xy"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1099 <param name="x" value="n_genes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1100 <param name="y" value="n_counts"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1101 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1102 <section name="plot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1103 <param name="legend_fontsize" value="1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1104 <param name="legend_fontweight" value="normal"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1105 <param name="palette" value="bwr"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1106 <param name="size" value="1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1107 <param name="title" value="A title"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1108 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1109 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1110 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1111 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1112 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1113 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1114 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1115 <has_text_matching expression="sc.pl.scatter"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1116 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1117 <has_text_matching expression="sort_order=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1118 <has_text_matching expression="projection='2d'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1119 <has_text_matching expression="legend_fontsize=1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1120 <has_text_matching expression="legend_fontweight='normal'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1121 <has_text_matching expression="frameon=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1122 <has_text_matching expression="size=1.0"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1123 <has_text_matching expression="title='A title'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1124 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1125 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1126 <output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1127 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1128
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1129 <!-- test 4 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1130 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1131 <param name="adata" value="krumsiek11.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1132 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1133 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1134 <param name="method" value="pl.heatmap"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1135 <param name="groupby" value="cell_type"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1136 <conditional name="figsize">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1137 <param name="custom" value="yes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1138 <param name="width" value="10"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1139 <param name="height" value="3"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1140 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1141 <param name="dendrogram" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1142 <param name="swap_axes" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1143 <section name="matplotlib_pyplot_imshow">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1144 <param name="cmap" value="YlGnBu"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1145 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1146 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1147 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1148 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1149 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1150 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1151 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1152 <has_text_matching expression="sc.pl.heatmap"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1153 <has_text_matching expression="var_names=adata.var_names"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1154 <has_text_matching expression="groupby='cell_type'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1155 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1156 <has_text_matching expression="use_raw=None"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1157 <has_text_matching expression="num_categories=7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1158 <has_text_matching expression="dendrogram=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1159 <has_text_matching expression="figsize=$10, 3$"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1160 <has_text_matching expression="swap_axes=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1161 <has_text_matching expression="show_gene_labels=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1162 <has_text_matching expression="cmap='YlGnBu'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1163 <has_text_matching expression="origin='upper'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1164 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1165 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1166 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1167 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1168
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1169 <!-- test 5 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1170 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1171 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1172 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1173 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1174 <param name="method" value="pl.heatmap"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1175 <conditional name="var_names">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1176 <param name="type" value="custom"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1177 <param name="var_names" value="Fog1,EKLF,SCL"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1178 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1179 <param name="gene_symbols" value="symbol"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1180 <param name="groupby" value="cell_type"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1181 <conditional name="figsize">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1182 <param name="custom" value="yes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1183 <param name="width" value="10"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1184 <param name="height" value="3"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1185 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1186 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1187 <param name="swap_axes" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1188 <param name="show_gene_labels" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1189 <section name="matplotlib_pyplot_imshow">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1190 <param name="cmap" value="YlGnBu"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1191 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1192 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1193 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1194 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1195 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1196 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1197 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1198 <has_text_matching expression="sc.pl.heatmap"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1199 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1200 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1201 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1202 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1203 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1204 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1205 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1206 <has_text_matching expression="figsize=$10, 3$"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1207 <has_text_matching expression="swap_axes=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1208 <has_text_matching expression="show_gene_labels=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1209 <has_text_matching expression="cmap='YlGnBu'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1210 <has_text_matching expression="origin='upper'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1211 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1212 </output>
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1213 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1214
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1215 <!-- test 6 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1216 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1217 <param name="adata" value="pbmc68k_reduced.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1218 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1219 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1220 <param name="method" value="pl.dotplot"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1221 <conditional name="var_names">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1222 <param name="type" value="custom"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1223 <param name="var_names" value="CD79A, MS4A1, CD8A, CD8B, LYZ, GNLY, NKG7, RP3-467N11.1, FCGR3A, FCER1A, CST3, POU2AF1, LINC00402"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1224 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1225 <param name="groupby" value="louvain"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1226 <param name="dendrogram" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1227 <repeat name="var_group_positions">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1228 <param name="start" value="0"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1229 <param name="end" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1230 <param name="label" value="B cells"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1231 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1232 <repeat name="var_group_positions">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1233 <param name="start" value="11"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1234 <param name="end" value="12"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1235 <param name="label" value="dendritic"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1236 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1237 <param name="color_map" value="hot"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1238 <param name="dot_max" value="0.7"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1239 <param name="dot_min" value="0.1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1240 <section name="matplotlib_pyplot_scatter">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1241 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1242 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1243 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1244 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1245 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1246 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1247 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1248 <has_text_matching expression="sc.pl.dotplot"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1249 <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1250 <has_text_matching expression="groupby='louvain'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1251 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1252 <has_text_matching expression="use_raw=None"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1253 <has_text_matching expression="num_categories=7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1254 <has_text_matching expression="dendrogram=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1255 <has_text_matching expression="var_group_positions=\[$0, 1$, $11, 12$\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1256 <has_text_matching expression="var_group_labels=\['B cells', 'dendritic'\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1257 <has_text_matching expression="color_map='hot'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1258 <has_text_matching expression="dot_max=0.7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1259 <has_text_matching expression="dot_min=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1260 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1261 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1262 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1263 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1264
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1265 <!-- test 7 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1266 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1267 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1268 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1269 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1270 <param name="method" value="pl.dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1271 <conditional name="var_names">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1272 <param name="type" value="custom"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1273 <param name="var_names" value="Fog1,EKLF,SCL"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1274 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1275 <param name="gene_symbols" value="symbol"/>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1276 <param name="groupby" value="cell_type"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1277 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1278 <section name="matplotlib_pyplot_imshow">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1279 <param name="cmap" value="YlGnBu"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1280 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1281 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1282 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1283 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1284 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1285 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1286 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1287 <has_text_matching expression="sc.pl.dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1288 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1289 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1290 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1291 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1292 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1293 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1294 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1295 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1296 </output>
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1297 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1298
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1299 <!-- test 8 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1300 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1301 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1302 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1303 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1304 <param name="method" value="pl.tracksplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1305 <param name="gene_symbols" value="symbol"/>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1306 <param name="groupby" value="cell_type"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1307 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1308 <section name="matplotlib_pyplot_imshow">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1309 <param name="cmap" value="YlGnBu"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1310 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1311 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1312 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1313 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1314 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1315 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1316 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1317 <has_text_matching expression="sc.pl.tracksplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1318 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1319 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1320 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1321 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1322 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1323 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1324 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1325 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1326 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1327
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1328 <!-- test 9 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1329 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1330 <param name="adata" value="pbmc68k_reduced.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1331 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1332 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1333 <param name="method" value="pl.violin"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1334 <conditional name="key_variables">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1335 <param name="type" value="custom"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1336 <param name="keys" value="n_genes, percent_mito, n_counts"/>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1337 </conditional>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1338 <section name="violin_plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1339 <conditional name="multi_panel">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1340 <param name="multi_panel" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1341 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1342 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1343 <section name="seaborn_violinplot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1344 <param name="linewidth" value="0"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1345 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1346 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1347 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1348 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1349 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1350 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1351 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1352 <has_text_matching expression="sc.pl.violin"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1353 <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1354 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1355 <has_text_matching expression="use_raw=None"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1356 <has_text_matching expression="stripplot=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1357 <has_text_matching expression="jitter=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1358 <has_text_matching expression="size=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1359 <has_text_matching expression="multi_panel=True"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1360 <has_text_matching expression="bw_method='scott'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1361 <has_text_matching expression="saturation=0.75"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1362 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1363 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1364 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="image_diff" eps="0.4"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1365 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1366
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1367 <!-- test 10 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1368 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1369 <param name="adata" value="krumsiek11.h5ad"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1370 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1371 <conditional name="method">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1372 <param name="method" value="pl.stacked_violin"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1373 <param name="groupby" value="cell_type"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1374 <param name="dendrogram" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1375 <param name="swap_axes" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1376 <section name="violin_plot">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1377 <param name="density_norm" value="width"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1378 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1379 <section name="seaborn_violinplot">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1380 <param name="linewidth" value="0"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1381 </section>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1382 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1383 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1384 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1385 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1386 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1387 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1388 <has_text_matching expression="sc.pl.stacked_violin"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1389 <has_text_matching expression="groupby='cell_type'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1390 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1391 <has_text_matching expression="use_raw=None"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1392 <has_text_matching expression="num_categories=7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1393 <has_text_matching expression="dendrogram=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1394 <has_text_matching expression="swap_axes=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1395 <has_text_matching expression="stripplot=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1396 <has_text_matching expression="jitter=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1397 <has_text_matching expression="size=1"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1398 <has_text_matching expression="density_norm='width'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1399 <has_text_matching expression="bw_method='scott'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1400 <has_text_matching expression="saturation=0.75"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1401 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1402 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1403 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="image_diff" eps="1.1"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1404 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1405
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1406 <!-- test 11 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1407 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1408 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1409 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1410 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1411 <param name="method" value="pl.stacked_violin"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1412 <conditional name="var_names">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1413 <param name="type" value="custom"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1414 <param name="var_names" value="Fog1,EKLF,SCL"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1415 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1416 <param name="gene_symbols" value="symbol"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1417 <param name="groupby" value="cell_type"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1418 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1419 <param name="swap_axes" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1420 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1421 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1422 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1423 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1424 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1425 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1426 <has_text_matching expression="sc.pl.stacked_violin"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1427 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1428 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1429 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1430 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1431 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1432 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1433 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1434 <has_text_matching expression="swap_axes=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1435 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1436 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1437 <output name="out_png" file="pl.stacked_violin_pp.filter_genes_dispersion.krumsiek11-seurat.png" compare="image_diff" eps="0.6"/>
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1438 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1439
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1440 <!-- test 12 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1441 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1442 <param name="adata" value="krumsiek11.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1443 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1444 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1445 <param name="method" value="pl.matrixplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1446 <param name="groupby" value="cell_type"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1447 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1448 <param name="swap_axes" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1449 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1450 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1451 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1452 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1453 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1454 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1455 <has_text_matching expression="sc.pl.matrixplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1456 <has_text_matching expression="var_names=adata.var_names"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1457 <has_text_matching expression="groupby='cell_type'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1458 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1459 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1460 <has_text_matching expression="num_categories=7"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1461 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1462 <has_text_matching expression="swap_axes=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1463 <has_text_matching expression="snap=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1464 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1465 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1466 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1467 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1468
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1469 <!-- test 13 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1470 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1471 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1472 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1473 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1474 <param name="method" value="pl.matrixplot"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1475 <conditional name="var_names">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1476 <param name="type" value="custom"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1477 <param name="var_names" value="Fog1,EKLF,SCL"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1478 </conditional>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1479 <param name="gene_symbols" value="symbol"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1480 <param name="groupby" value="cell_type"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1481 <conditional name="figsize">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1482 <param name="custom" value="yes"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1483 <param name="width" value="10"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1484 <param name="height" value="3"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1485 </conditional>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1486 <param name="dendrogram" value="True"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1487 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1488 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1489 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1490 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1491 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1492 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1493 <has_text_matching expression="sc.pl.matrixplot"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1494 <has_text_matching expression="gene_symbols='symbol'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1495 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1496 <has_text_matching expression="groupby='cell_type'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1497 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1498 <has_text_matching expression="use_raw=None"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1499 <has_text_matching expression="num_categories=7"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1500 <has_text_matching expression="dendrogram=True"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1501 <has_text_matching expression="swap_axes=False"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1502 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1503 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1504 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1505
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1506 <!-- test 14 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1507 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1508 <param name="adata" value="krumsiek11.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1509 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1510 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1511 <param name="method" value="pl.clustermap"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1512 <section name="seaborn_clustermap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1513 <param name="method" value="single"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1514 <param name="col_cluster" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1515 <param name="row_cluster" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1516 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1517 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1518 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1519 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1520 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1521 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1522 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1523 <has_text_matching expression="sc.pl.clustermap"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1524 <has_text_matching expression="adata=adata"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1525 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1526 <has_text_matching expression="method='single'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1527 <has_text_matching expression="metric='euclidean'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1528 <has_text_matching expression="col_cluster=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1529 <has_text_matching expression="row_cluster=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1530 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1531 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1532 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1533 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1534
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1535 <!-- test 15 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1536 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1537 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1538 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1539 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1540 <param name="method" value="pl.highest_expr_genes"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1541 <param name="gene_symbols" value="symbol"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1542 <section name="setseaborn_boxplot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1543 <param name="color" value="blue"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1544 <param name="saturation" value="0.5"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1545 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1546 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1547 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1548 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1549 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1550 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1551 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1552 <has_text_matching expression="sc.pl.highest_expr_genes"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1553 <has_text_matching expression="n_top=30"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1554 <has_text_matching expression="gene_symbols='symbol'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1555 <has_text_matching expression="color='blue'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1556 <has_text_matching expression="saturation=0.5"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1557 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1558 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1559 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1560 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1561
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1562 <!-- test 16 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1563 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1564 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1565 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1566 <conditional name="method">
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1567 <param name="method" value="pl.highly_variable_genes"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1568 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1569 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1570 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1571 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1572 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1573 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1574 <has_text_matching expression="sc.pl.highly_variable_genes"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1575 <has_text_matching expression="adata_or_result=adata"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1576 <has_text_matching expression="log=False"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1577 <has_text_matching expression="highly_variable_genes=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1578 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1579 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1580 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="image_diff"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1581 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1582
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1583 <!-- test 17 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1584 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1585 <param name="adata" value="pp.scrublet.krumsiek11.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1586 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1587 <conditional name="method">
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1588 <param name="method" value="pl.scrublet_score_distribution"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1589 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1590 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1591 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1592 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1593 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1594 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1595 <has_text_matching expression="sc.pl.scrublet_score_distribution"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1596 <has_text_matching expression="adata=adata"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1597 <has_text_matching expression="scale_hist_obs='log'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1598 <has_text_matching expression="scale_hist_sim='linear'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1599 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1600 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1601 <output name="out_png" file="pl.scrublet_score_distribution.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1602 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1603
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1604 <!-- test 18 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1605 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1606 <param name="adata" value="pbmc68k_reduced.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1607 <param name="format" value="pdf"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1608 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1609 <param name="method" value="pl.pca"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1610 <param name="color" value="CD3D,CD79A"/>
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	1611 <param name="gene_symbols" value="symbol"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1612 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1613 <repeat name="components">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1614 <param name="axis1" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1615 <param name="axis2" value="2"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1616 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1617 <repeat name="components">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1618 <param name="axis1" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1619 <param name="axis2" value="3"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1620 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1621 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1622 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1623 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1624 <param name="ncols" value="2"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1625 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1626 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1627 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1628 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1629 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1630 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1631 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1632 <has_text_matching expression="sc.pl.pca"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1633 <has_text_matching expression="save='.pdf'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1634 <has_text_matching expression="color=\['CD3D', 'CD79A'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1635 <has_text_matching expression="use_raw=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1636 <has_text_matching expression="sort_order=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1637 <has_text_matching expression="components=\['1,2', '1,3'\]"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1638 <has_text_matching expression="projection='2d'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1639 <has_text_matching expression="legend_loc='right margin'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1640 <has_text_matching expression="legend_fontsize=1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1641 <has_text_matching expression="legend_fontweight='normal'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1642 <has_text_matching expression="size=1.0"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1643 <has_text_matching expression="frameon=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1644 <has_text_matching expression="ncols=2"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1645 <has_text_matching expression="wspace=0.1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1646 <has_text_matching expression="hspace=0.25"/>
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	1647 <has_text_matching expression="gene_symbols='symbol'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1648 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1649 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1650 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1651 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1652
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1653 <!-- test 19 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1654 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1655 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1656 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1657 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1658 <param name="method" value="pl.pca_loadings"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1659 <param name="components" value="1,2,3"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1660 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1661 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1662 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1663 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1664 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1665 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1666 <has_text_matching expression="sc.pl.pca_loadings"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1667 <has_text_matching expression="components=\[1, 2, 3\]"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1668 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1669 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1670 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1671 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1672
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1673 <!-- test 20 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1674 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1675 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1676 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1677 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1678 <param name="method" value="pl.pca_variance_ratio"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1679 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1680 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1681 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1682 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1683 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1684 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1685 <has_text_matching expression="sc.pl.pca_variance_ratio"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1686 <has_text_matching expression="log=False"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1687 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1688 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1689 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1690 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1691
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1692 <!-- test 21 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1693 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1694 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1695 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1696 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1697 <param name="method" value="pl.pca_overview"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1698 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1699 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1700 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1701 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1702 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1703 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1704 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1705 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1706 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1707 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1708 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1709 <has_text_matching expression="sc.pl.pca_overview"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1710 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1711 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1712 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1713 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1714 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1715 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1716 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1717 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1718 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1719 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1720 <has_text_matching expression="hspace=0.25"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1721 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1722 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1723 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1724 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1725
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1726 <!-- test 22 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1727 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1728 <param name="adata" value="tl.tsne.krumsiek11.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1729 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1730 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1731 <param name="method" value="pl.tsne"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1732 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1733 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1734 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1735 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1736 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1737 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1738 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1739 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1740 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1741 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1742 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1743 <has_text_matching expression="sc.pl.tsne"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1744 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1745 <has_text_matching expression="edges=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1746 <has_text_matching expression="arrows=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1747 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1748 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1749 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1750 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1751 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1752 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1753 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1754 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1755 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1756 <has_text_matching expression="hspace=0.25"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1757 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1758 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1759 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1760 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1761
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1762 <!-- test 23 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1763 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1764 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1765 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1766 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1767 <param name="method" value="pl.umap"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1768 <param name="color" value="paul15_clusters"/>
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	1769 <param name="gene_symbols" value="symbol"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1770 <conditional name="edges">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1771 <param name="edges" value="True"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1772 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1773 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1774 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1775 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1776 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1777 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1778 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1779 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1780 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1781 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1782 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1783 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1784 <has_text_matching expression="sc.pl.umap"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1785 <has_text_matching expression="color=\['paul15_clusters'\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1786 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1787 <has_text_matching expression="edges=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1788 <has_text_matching expression="edges_width=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1789 <has_text_matching expression="arrows=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1790 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1791 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1792 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1793 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1794 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1795 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1796 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1797 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1798 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1799 <has_text_matching expression="hspace=0.25"/>
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	1800 <has_text_matching expression="gene_symbols='symbol'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1801 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1802 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1803 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1804 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1805
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1806 <!-- test 24 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1807 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1808 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1809 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1810 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1811 <param name="method" value="pl.diffmap"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1812 <param name="color" value="paul15_clusters"/>
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	1813 <param name="gene_symbols" value="symbol"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1814 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1815 <param name="legend_fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1816 <param name="legend_fontweight" value="normal"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1817 <param name="size" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1818 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1819 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1820 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1821 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1822 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1823 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1824 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1825 <has_text_matching expression="sc.pl.diffmap"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1826 <has_text_matching expression="color=\['paul15_clusters'\]"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1827 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1828 <has_text_matching expression="sort_order=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1829 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1830 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1831 <has_text_matching expression="legend_fontsize=1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1832 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1833 <has_text_matching expression="size=1.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1834 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1835 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1836 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1837 <has_text_matching expression="hspace=0.25"/>
20 62acdd96d4a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 55ba4cd74d5d8f7baff164b1864c36759d1c7fd9 iuc parents: 19 diff changeset	1838 <has_text_matching expression="gene_symbols='symbol'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1839 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1840 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1841 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1842 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1843
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1844 <!-- test 25 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1845 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1846 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1847 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1848 <conditional name="method">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1849 <param name="method" value="pl.draw_graph"/>
8 6adf98e782f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec" iuc parents: 7 diff changeset	1850 <param name="layout" value="fr"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1851 <conditional name="edges">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1852 <param name="edges" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1853 <param name="edges_color" value="Crimson"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1854 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1855 <param name="sort_order" value="false"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1856 <section name="plot">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1857 <param name="legend_fontweight" value="normal"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1858 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1859 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1860 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1861 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1862 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1863 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1864 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1865 <has_text_matching expression="sc.pl.draw_graph"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1866 <has_text_matching expression="use_raw=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1867 <has_text_matching expression="edges=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1868 <has_text_matching expression="edges_width=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1869 <has_text_matching expression="edges_color='Crimson'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1870 <has_text_matching expression="arrows=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1871 <has_text_matching expression="sort_order=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1872 <has_text_matching expression="projection='2d'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1873 <has_text_matching expression="legend_loc='right margin'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1874 <has_text_matching expression="legend_fontweight='normal'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1875 <has_text_matching expression="frameon=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1876 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1877 <has_text_matching expression="wspace=0.1"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1878 <has_text_matching expression="hspace=0.25"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1879 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1880 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1881 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="image_diff"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1882 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1883
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1884 <!-- test 26 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1885 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1886 <param name="adata" value="tl.embedding_density.umap.pbmc68k_reduced.h5ad"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1887 <param name="format" value="png"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1888 <conditional name="method">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1889 <param name="method" value="pl.embedding_density"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1890 <param name="key" value="umap_density_bulk_labels"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1891 </conditional>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1892 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1893 <param name="show_log" value="true"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1894 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1895 <output name="hidden_output">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1896 <assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1897 <has_text_matching expression="sc.pl.embedding_density"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1898 <has_text_matching expression="basis='umap'"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1899 <has_text_matching expression="key='umap_density_bulk_labels'"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1900 </assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1901 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1902 <output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1903 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1904
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1905 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1906 <!-- test 27 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1907 <!-- <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1908 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1909 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1910 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1911 <param name="method" value="pl.dpt_groups_pseudotime"/>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1912
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1913 </conditional>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1914 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1915 <param name="show_log" value="true"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1916 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1917 <output name="hidden_output">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1918 <assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1919 <has_text_matching expression="sc.pl.dpt_groups_pseudotime"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1920 <has_text_matching expression="color_map='viridis'"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1921 </assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1922 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1923 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1924 </test> -->
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1925
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1926 <!-- test 28 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1927 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1928 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1929 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1930 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1931 <param name="method" value="pl.dpt_timeseries"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1932 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1933 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1934 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1935 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1936 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1937 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1938 <has_text_matching expression="sc.pl.dpt_timeseries"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1939 <has_text_matching expression="as_heatmap=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1940 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1941 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1942 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1943 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1944
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1945 <!-- test 29 -->
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1946 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1947 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1948 <param name="format" value="png"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1949 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1950 <param name="method" value="pl.paga"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1951 <param name="threshold" value="0.01"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1952 <param name="color" value="louvain"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1953 <param name="layout" value="fr"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1954 <param name="fontsize" value="1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1955 <param name="edge_width_scale" value="5"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1956 </conditional>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1957 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1958 <output name="anndata_out" ftype="h5ad">
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1959 <assert_contents>
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1960 <has_h5_keys keys="uns/paga"/>
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1961 </assert_contents>
40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1962 </output>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1963 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1964
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1965 <!-- test 30 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1966 <test expect_num_outputs="1">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1967 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1968 <param name="format" value="png"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1969 <conditional name="method">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1970 <param name="method" value="pl.paga_compare"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1971 <param name="threshold" value="0.01"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1972 <param name="color" value="louvain"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1973 <param name="layout" value="fr"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1974 <param name="fontsize" value="1"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1975 <param name="edge_width_scale" value="5"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1976 </conditional>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1977 <output name="out_png" file="pl.paga_compare.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1978 </test>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1979
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1980 <!-- test 31 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1981 <!-- <test expect_num_outputs="2">
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1982 test pl.paga_path
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1983 </test> -->
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1984
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1985 <!-- test 32 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1986 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1987 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1988 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1989 <conditional name="method">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1990 <param name="method" value="pl.rank_genes_groups"/>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	1991 <param name="n_genes" value="10"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1992 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1993 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	1994 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1995 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1996 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1997 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1998 <has_text_matching expression="sc.pl.rank_genes_groups"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1999 <has_text_matching expression="n_genes=10"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2000 <has_text_matching expression="fontsize=8"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2001 <has_text_matching expression="ncols=4"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2002 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2003 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2004 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2005 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	2006
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2007 <!-- test 33 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2008 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2009 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2010 <param name="format" value="png"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2011 <conditional name="method">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2012 <param name="method" value="pl.rank_genes_groups_violin"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2013 <conditional name="genes">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2014 <param name="select" value="n_genes"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2015 <param name="n_genes" value="10"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2016 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2017 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2018 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2019 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2020 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2021 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2022 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2023 <has_text_matching expression="sc.pl.rank_genes_groups_violin"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2024 <has_text_matching expression="n_genes=10"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2025 <has_text_matching expression="use_raw=None"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2026 <has_text_matching expression="split=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2027 <has_text_matching expression="strip=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2028 <has_text_matching expression="jitter=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2029 <has_text_matching expression="size=1"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2030 <has_text_matching expression="density_norm='width'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2031 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2032 </output>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2033 <output_collection name="collection_png">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2034 <element name="cell_type_Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="image_diff" eps="3.5"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2035 <element name="cell_type_Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="image_diff" eps="3.5"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2036 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="image_diff" eps="3.5"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2037 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="image_diff" eps="3.5"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2038 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="image_diff" eps="3.5"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2039 </output_collection>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2040 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	2041
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2042 <!-- test 34 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2043 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2044 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2045 <param name="format" value="png"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2046 <conditional name="method">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2047 <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2048 <param name="n_genes" value="10"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2049 <param name="dendrogram" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2050 <param name="swap_axes" value="True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2051 <section name="violin_plot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2052 <conditional name="stripplot">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2053 <param name="size" value="1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2054 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2055 <param name="density_norm" value="width"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2056 </section>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2057 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2058 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2059 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2060 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2061 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2062 <assert_contents>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2063 <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2064 <has_text_matching expression="n_genes=10"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2065 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2066 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2067 <has_text_matching expression="dendrogram=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2068 <has_text_matching expression="swap_axes=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2069 <has_text_matching expression="stripplot=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2070 <has_text_matching expression="jitter=True"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2071 <has_text_matching expression="size=1"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2072 <has_text_matching expression="density_norm='width'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2073 <has_text_matching expression="bw_method='scott'"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2074 <has_text_matching expression="saturation=0.75"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2075 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2076 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2077 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff" eps="1.5"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2078 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	2079
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2080 <!-- test 35 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2081 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2082 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2083 <param name="format" value="png"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2084 <conditional name="method">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2085 <param name="method" value="pl.rank_genes_groups_heatmap"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2086 <param name="n_genes" value="10"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2087 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2088 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2089 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2090 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2091 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2092 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2093 <has_text_matching expression="sc.pl.rank_genes_groups_heatmap"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2094 <has_text_matching expression="n_genes=10"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2095 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2096 <has_text_matching expression="use_raw=None"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2097 <has_text_matching expression="dendrogram=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2098 <has_text_matching expression="swap_axes=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2099 <has_text_matching expression="show_gene_labels=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2100 <has_text_matching expression="origin='upper'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2101 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2102 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2103 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2104 </test>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2105
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2106 <!-- test 36 -->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2107 <test expect_num_outputs="2">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2108 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2109 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2110 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2111 <param name="method" value="pl.rank_genes_groups_dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2112 <param name="n_genes" value="10"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2113 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2114 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2115 <param name="show_log" value="true"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2116 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2117 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2118 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2119 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2120 <has_text_matching expression="n_genes=10"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2121 <has_text_matching expression="log=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2122 <has_text_matching expression="use_raw=None"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2123 <has_text_matching expression="dendrogram=False"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2124 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2125 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2126 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2127 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	2128
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2129 <!-- test 37 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2130 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2131 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2132 <param name="format" value="png"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2133 <conditional name="method">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2134 <param name="method" value="pl.rank_genes_groups_matrixplot"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2135 <param name="n_genes" value="10"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2136 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2137 <section name="advanced_common">
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2138 <param name="show_log" value="true"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2139 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2140 <output name="hidden_output">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2141 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2142 <has_text_matching expression="sc.pl.rank_genes_groups_matrixplot"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2143 <has_text_matching expression="n_genes=10"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2144 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2145 <has_text_matching expression="use_raw=None"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2146 <has_text_matching expression="dendrogram=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2147 <has_text_matching expression="swap_axes=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2148 <has_text_matching expression="snap=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2149 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2150 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2151 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2152 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	2153
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2154 <!-- test 38 pl.rank_genes_groups_dotplot with marker list-->
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2155 <test expect_num_outputs="2">
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2156 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2157 <param name="format" value="png"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2158 <conditional name="method">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2159 <param name="method" value="pl.rank_genes_groups_dotplot"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2160 <conditional name="var_names">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2161 <param name="type" value="customfile"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2162 <param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.tsv"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2163 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2164 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2165 <section name="advanced_common">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2166 <param name="show_log" value="true" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2167 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2168 <output name="hidden_output">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2169 <assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2170 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2171 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2172 <has_text_matching expression="use_raw=None"/>
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2173 <has_text_matching expression="dendrogram=False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2174 </assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2175 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2176 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="image_diff"/>
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2177 </test>
19 40812a65a78b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f iuc parents: 17 diff changeset	2178
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2179 <!-- test 39: pl.rank_genes_groups_dotplot with marker list -->
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2180 <test expect_num_outputs="2">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2181 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2182 <param name="format" value="png"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2183 <conditional name="method">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2184 <param name="method" value="pl.rank_genes_groups_dotplot"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2185 <conditional name="var_names">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2186 <param name="type" value="customfile"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2187 <param name="var_names" value="tl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.tsv"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2188 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2189 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2190 <section name="advanced_common">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2191 <param name="show_log" value="true" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2192 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2193 <output name="hidden_output">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2194 <assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2195 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2196 <has_text_matching expression="log=False"/>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2197 <has_text_matching expression="use_raw=None"/>
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2198 <has_text_matching expression="dendrogram=False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2199 </assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2200 </output>
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2201 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="image_diff"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2202 </test>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2203
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2204 <!-- test 40 -->
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2205 <test expect_num_outputs="2">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2206 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2207 <param name="format" value="png"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2208 <conditional name="method">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2209 <param name="method" value="pl.rank_genes_groups_tracksplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2210 </conditional>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2211 <section name="advanced_common">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2212 <param name="show_log" value="true" />
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2213 </section>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2214 <output name="hidden_output">
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2215 <assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2216 <has_text_matching expression="sc.pl.rank_genes_groups_tracksplot"/>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2217 </assert_contents>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2218 </output>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2219 <output name="out_png" file="pl.rank_genes_groups_tracksplot.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="image_diff"/>
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2220 </test>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2221 </tests>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2222 <help><![CDATA[
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2223 Generic: Scatter plot along observations or variables axes (`pl.scatter`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2224 =========================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2225
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2226 Color the plot using annotations of observations (`.obs`), variables
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2227 (`.var`) or expression of genes (`.var_names`).
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2228
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2229 More details on the `scanpy documentation
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2230 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.scatter.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2231
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2232 Generic: Heatmap of the expression values of set of genes (`pl.heatmap`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2233 ========================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2234
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2235 If `groupby` is given, the heatmap is ordered by the respective group. For
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2236 example, a list of marker genes can be plotted, ordered by clustering. If
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2237 the `groupby` observation annotation is not categorical the observation
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2238 annotation is turned into a categorical by binning the data into the number
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2239 specified in `num_categories`.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2240
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2241 More details on the `scanpy documentation
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2242 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.heatmap.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2243
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2244 Generic: Makes a dot plot of the expression values (`pl.dotplot`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2245 =================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2246
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2247 For each var_name and each `groupby` category a dot is plotted. Each dot
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2248 represents two values: mean expression within each category (visualized by
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2249 color) and fraction of cells expressing the var_name in the
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2250 category. (visualized by the size of the dot). If groupby is not given, the
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2251 dotplot assumes that all data belongs to a single category. A gene is not
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2252 considered expressed if the expression value in the adata (or adata.raw) is
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2253 equal to zero.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2254
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2255 For instance, for each marker gene, the mean value and the percentage of cells
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2256 expressing the gene can be visualized for each cluster.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2257
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2258 More details on the `scanpy documentation
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2259 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.dotplot.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2260
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2261 Generic: Tracks plot (`pl.tracksplot`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2262 ======================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2263
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2264 In this type of plot each var_name is plotted as a filled line plot where the y values correspond to the var_name values and x is each of the cells.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2265 Best results are obtained when using raw counts that are not log.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2266
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2267 More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2268 <https://scanpy.readthedocs.io/en/stable/generated/scanpy.pl.tracksplot.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2269
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2270 Generic: Violin plot (`pl.violin`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2271 ==================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2272
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2273 Wraps `seaborn.violinplot` for `anndata.AnnData`.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2274
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2275 More details on the `scanpy documentation
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2276 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.violin.html>`__
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2277
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2278 Generic: Stacked violin plots (`pl.stacked_violin`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2279 ===================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2280
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2281 Makes a compact image composed of individual violin plots (from `seaborn.violinplot`)
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2282 stacked on top of each other. Useful to visualize gene expression per cluster.
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2283
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2284 More details on the `scanpy documentation
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2285 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.stacked_violin.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2286
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2287 Generic: Heatmap of the mean expression values per cluster (`pl.matrixplot`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2288 ============================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2289
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2290 Creates a heatmap of the mean expression values per cluster of each var_names
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2291
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2292 If groupby is not given, the matrixplot assumes that all data belongs to a single
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2293 category.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2294
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2295 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2296 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.matrixplot.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2297
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2298 Generic: Hierarchically-clustered heatmap (`pl.clustermap`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2299 ===========================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2300
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2301 Wraps `seaborn.clustermap
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2302 <https://seaborn.pydata.org/generated/seaborn.clustermap.html>`__ for
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2303 `anndata.AnnData`.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2304
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2305 The returned object has a savefig() method that should be used if you want
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2306 to save the figure object without clipping the dendrograms.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2307
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2308 To access the reordered row indices, use:
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2309 clustergrid.dendrogram_row.reordered_ind
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2310
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2311 Column indices, use: clustergrid.dendrogram_col.reordered_ind
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2312
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2313 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2314 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pl.clustermap.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2315
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2316 Preprocessing: Plot the fraction of counts assigned to each gene over all cells (`pl.highest_expr_genes`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2317 =========================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2318
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2319 Computes, for each gene, the fraction of counts assigned to that gene within
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2320 a cell. The `n_top` genes with the highest mean fraction over all cells are
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2321 plotted as boxplots.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2322
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2323 This plot is similar to the `scater` package function `plotHighestExprs(type= "highest-expression")`
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2324
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2325 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2326 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highest_expr_genes.html>`__
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2327
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2328 Preprocessing: Plot dispersions versus means for genes (`pl.highly_variable_genes`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2329 ===================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2330
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2331 It produces Supp. Fig. 5c of Zheng et al. (2017) and MeanVarPlot() of Seurat.
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2332
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2333 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2334 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.highly_variable_genes.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2335
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2336 Preprocessing: Plot histogram of doublet scores for observed transcriptomes and simulated doublets (`pl.scrublet_score_distribution`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2337 =====================================================================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2338
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2339 The histogram for simulated doublets is useful for determining the correct doublet score threshold.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2340 Scrublet must have been run previously with the input object.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2341
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2342 More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2343 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.scrublet_score_distribution.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2344
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2345 PCA: Scatter plot in PCA coordinates (`pl.pca`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2346 ===============================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2347
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2348 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2349 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2350
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2351 PCA: Rank genes according to contributions to PCs (`pl.pca_loadings`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2352 =====================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2353
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2354 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2355 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_loadings.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2356
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2357 PCA: Plot the variance ratio (`pl.pca_variance_ratio`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2358 ======================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2359
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2360 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2361 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_variance_ratio.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2362
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2363 PCA: Plot PCA results (`pl.pca_overview`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2364 =========================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2365
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2366 The parameters are the ones of the scatter plot. Call pca_ranking separately
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2367 if you want to change the default settings.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2368
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2369 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2370 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.pca_overview.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2371
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2372 Embedding: Scatter plot in tSNE basis (`pl.tsne`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2373 =================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2374
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2375 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2376 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.tsne.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2377
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2378 Embeddings: Scatter plot in UMAP basis (`pl.umap`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2379 ==================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2380
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2381 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2382 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.umap.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2383
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2384 Embeddings: Scatter plot in Diffusion Map basis (`pl.diffmap`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2385 ==============================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2386
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2387 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2388 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.diffmap.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2389
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2390 Embeddings: Scatter plot in graph-drawing basis (`pl.draw_graph`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2391 =================================================================
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2392
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2393 More details on the `scanpy documentation
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2394 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.draw_graph.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2395
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2396 Embeddings: Plot the density of cells in an embedding (per condition) (`pl.embedding_density`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2397 ==============================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2398
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2399 More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2400 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.embedding_density.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2401
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2402 .. This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed.
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2403 .. Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2404 .. ===========================================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2405
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2406 .. More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2407 .. <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_groups_pseudotime.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2408
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2409 Branching trajectories and pseudotime, clustering: Heatmap of pseudotime series (`pl.dpt_timeseries`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2410 =====================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2411
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2412 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2413 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.dpt_timeseries.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2414
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2415
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2416 Branching trajectories and pseudotime, clustering: Plot the abstracted graph through thresholding low-connectivity edges (`pl.paga`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2417 ====================================================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2418
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2419 This uses ForceAtlas2 or igraph's layout algorithms for most layouts.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2420
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2421 When initializing the positions, note that - for some reason - igraph
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2422 mirrors coordinates along the x axis... that is, you should increase the
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2423 `maxiter` parameter by 1 if the layout is flipped.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2424
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2425 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2426 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2427
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2428
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2429 Branching trajectories and pseudotime, clustering: Scatter and PAGA graph side-by-side (`pl.paga_compare`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2430 ==========================================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2431
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2432 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2433 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_compare.html>`__
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2434
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2435 Branching trajectories and pseudotime, clustering: Gene expression and annotation changes along paths (`pl.paga_path`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2436 ======================================================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2437
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2438 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2439 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.paga_path.html>`__
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2440
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2441 Marker genes: Plot ranking of genes using dotplot plot (`pl.rank_genes_groups`)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2442 ===============================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2443
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2444 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2445 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups.html>`__
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2446
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2447 Marker genes: Plot ranking of genes as violin plot (`pl.rank_genes_groups_violin`)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2448 ==================================================================================
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2449
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2450 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2451 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_violin.html>`__
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2452
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2453 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2454 ==================================================================================================
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2455
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2456 More details on the `scanpy documentation
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2457 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_stacked_violin.html>`__
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2458
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2459 Marker genes: Plot ranking of genes as heatmap plot (`pl.rank_genes_groups_heatmap`)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2460 ====================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2461
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2462 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2463 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_heatmap.html>`__
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2464
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2465 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2466 ====================================================================================
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2467
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2468 More details on the `scanpy documentation
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2469 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_dotplot.html>`__
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2470
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2471 Marker genes: Plot ranking of genes as matrixplot plot (`pl.rank_genes_groups_matrixplot`)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2472 ==========================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2473
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2474 More details on the `scanpy documentation
14 f7446fd8d5e7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de iuc parents: 12 diff changeset	2475 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_matrixplot.html>`__
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2476
17 2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2477 ]]>
2dfb2227a16c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 91121b1e72696f17478dae383badaa71e9f96dbb iuc parents: 16 diff changeset	2478 </help>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2479 <expand macro="citations"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2480 </tool>

Mercurial > repos > iuc > scanpy_plot

annotate plot.xml @ 20:62acdd96d4a0 draft default tip