scanpy_plot: plot.xml annotate

annotate plot.xml @ 16:1072ce66b426 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0

author	iuc
date	Tue, 20 Aug 2024 09:53:51 +0000
parents	f7446fd8d5e7
children	2dfb2227a16c

rev	line source
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1 <tool id="scanpy_plot" name="Plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@profile@">
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2 <description> with scanpy</description>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	3 <macros>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	4 <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	5 </macros>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	6 <expand macro="bio_tools"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	7 <expand macro="requirements"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	8 <stdio>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	9 <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	10 </stdio>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	11 <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	12 <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	13 @CMD@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	14 ]]></command>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	15 <configfiles>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	16 <configfile name="script_file"><![CDATA[
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	17 @CMD_imports@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	18 @CMD_read_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	19
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	20 sc.settings.figdir = '.'
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	21
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	22 #if $method.method == 'pl.scatter'
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	23
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	24 #if $method.type.type == 'xy':
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	25 x_field='$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	26 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	27
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	28 #if $method.type.log:
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	29 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	30 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	31 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	32 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	33 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	34 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	35
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	36 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	37 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	38 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	39 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	40 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	41 y_field=f"log_{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 #end if
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	43 #end if
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	44
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	45 sc.pl.scatter(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	46 @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	47 #if $method.type.type == 'xy':
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	48 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	49 y=y_field,
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	50 #if $method.type.color
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	51 color='$method.type.color',
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	52 #end if
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	53 #if str('$method.type.layers.use_layers') == 'true'
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	54 layers=('$method.type.layers.layer_x', '$method.type.layers.layer_y', '$method.type.layers.layer_color'),
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	55 #end if
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	56 #else
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	57 basis='$method.type.basis',
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	58 #if $method.type.color
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	59 #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	60 color=$color,
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	61 #end if
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	62 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	63 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	64 sort_order=$method.sort_order,
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	65 @CMD_params_groups@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	66 @CMD_params_pl_components@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	67 projection='$method.plot.projection',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	68 legend_loc='$method.plot.legend_loc',
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	69 #if $method.plot.palette
8 6adf98e782f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec" iuc parents: 7 diff changeset	70 palette=['$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	71 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	72 #if $method.plot.color_map
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	73 color_map='$method.plot.color_map',
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	74 #end if
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	75 @CMD_param_legend_fontsize@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	76 legend_fontweight='$method.plot.legend_fontweight',
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	77 @CMD_param_title@
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	78 @CMD_param_size@
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	79 frameon=$method.plot.frameon)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	80
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	81 #else if $method.method == 'pl.heatmap'
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	82 @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	83 sc.pl.heatmap(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	84 @CMD_param_plot_inputs@
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	85 #if $method.gene_symbols
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	86 gene_symbols='$method.gene_symbols',
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	87 #end if
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	88 @CMD_params_inputs@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	89 @CMD_params_plots@
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	90 @CMD_pl_heatmap@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	91
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	92 #else if $method.method == 'pl.dotplot'
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	93 @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	94 sc.pl.dotplot(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	95 @CMD_param_plot_inputs@
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	96 #if $method.gene_symbols
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	97 gene_symbols='$method.gene_symbols',
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	98 #end if
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	99 @CMD_params_inputs@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	100 @CMD_params_plots@
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	101 @CMD_pl_dotplot@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	102
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	103 #else if $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	104 sc.pl.violin(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	105 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	106 #if $method.key_variables.type == "var_names"
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	107 #set $key_list = adata.var_names
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	108 #else if $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	109 #set $key_list = adata.obs.select_dtypes(exclude=['category']).columns
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	110 #else if $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	111 #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	112 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	113 keys=$key_list,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	114 #if $method.groupby
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	115 groupby='$method.groupby',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	116 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	117 log=$method.log,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	118 use_raw=$method.use_raw,
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	119 @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	120 multi_panel=$method.violin_plot.multi_panel.multi_panel,
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	121 #if $method.violin_plot.multi_panel.multi_panel == "True" and str($method.violin_plot.multi_panel.width) != '' and str($method.violin_plot.multi_panel.height) != ''
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	122 figsize=($method.violin_plot.multi_panel.width, $method.violin_plot.multi_panel.height),
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	123 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	124 scale='$method.violin_plot.scale',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	125 #if $method.xlabel
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	126 xlabel='$method.xlabel',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	127 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	128 #if str($method.rotation) != ''
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	129 rotation=$method.rotation,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	130 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	131 @CMD_params_seaborn_violinplot@)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	132
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	133 #else if $method.method == 'pl.stacked_violin'
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	134 @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	135 sc.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	136 @CMD_param_plot_inputs@
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	137 #if $method.gene_symbols
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	138 gene_symbols='$method.gene_symbols',
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	139 #end if
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	140 @CMD_params_inputs@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	141 @CMD_params_plots@
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	142 @CMD_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	143
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	144 #else if $method.method == 'pl.matrixplot'
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	145 @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	146 sc.pl.matrixplot(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	147 @CMD_param_plot_inputs@
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	148 #if $method.gene_symbols
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	149 gene_symbols='$method.gene_symbols',
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	150 #end if
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	151 @CMD_params_inputs@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	152 @CMD_params_plots@
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	153 @CMD_pl_matrixplot@)
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	154
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	155 #else if $method.method == 'pl.clustermap'
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	156 sc.pl.clustermap(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	157 #if str($method.use_raw) == 'True'
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	158 adata=adata.X,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	159 #else
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	160 adata=adata,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	161 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	162 show=False,
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	163 #if $method.obs_keys
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	164 obs_keys='$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	165 #end if
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	166 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	167 method='$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	168 metric='$method.seaborn_clustermap.metric',
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	169 #if str($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	170 z_score=$method.seaborn_clustermap.z_score,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	171 #end if
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	172 #if str($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	173 standard_scale=$method.seaborn_clustermap.standard_scale,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	174 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	175 col_cluster=$method.seaborn_clustermap.col_cluster,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	176 row_cluster=$method.seaborn_clustermap.row_cluster).savefig(fname="output.$format")
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	177
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	178 #else if $method.method == 'pl.highest_expr_genes'
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	179 sc.pl.highest_expr_genes(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	180 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	181 n_top=$method.n_top,
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	182 #if $method.gene_symbols
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	183 gene_symbols='$method.gene_symbols',
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	184 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	185 #if $method.setseaborn_boxplot.color
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	186 color='$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	187 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	188 #if $method.setseaborn_boxplot.palette
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	189 palette='$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	190 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	191 saturation=$method.setseaborn_boxplot.saturation)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	192
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	193 #else if $method.method == 'pl.highly_variable_genes'
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	194 sc.pl.highly_variable_genes(
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	195 adata_or_result=adata,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	196 log=$method.log,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	197 save='.$format',
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	198 show=False,
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	199 highly_variable_genes=$method.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	200
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	201 #else if $method.method == 'pl.pca'
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	202 sc.pl.pca(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	203 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	204 @CMD_param_color@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	205 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	206 sort_order=$method.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	207 @CMD_params_groups@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	208 @CMD_params_pl_components@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	209 @CMD_pl_attribute_section@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	210 @CMD_params_matplotlib_pyplot_scatter@)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	211
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	212 #else if $method.method == 'pl.pca_loadings'
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	213 sc.pl.pca_loadings(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	214 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	215 #set $components = ([int(x.strip()) for x in str($method.components).split(',')])
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	216 components=$components)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	217
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	218 #else if $method.method == 'pl.pca_variance_ratio'
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	219 sc.pl.pca_variance_ratio(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	220 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	221 n_pcs=$method.n_pcs,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	222 log=$method.log)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	223
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	224 #else if $method.method == 'pl.pca_overview'
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	225 sc.pl.pca_overview(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	226 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	227 @CMD_param_color@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	228 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	229 sort_order=$method.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	230 @CMD_params_groups@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	231 @CMD_params_pl_components@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	232 @CMD_pl_attribute_section@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	233 @CMD_params_matplotlib_pyplot_scatter@)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	234
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	235 #else if $method.method == 'pl.tsne'
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	236 sc.pl.tsne(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	237 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	238 @CMD_param_color@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	239 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	240 @CMD_pl_edges@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	241 arrows=$method.arrows,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	242 sort_order=$method.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	243 @CMD_params_groups@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	244 @CMD_params_pl_components@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	245 @CMD_pl_attribute_section@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	246 @CMD_params_matplotlib_pyplot_scatter@)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	247
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	248 #else if $method.method == 'pl.umap'
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	249 sc.pl.umap(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	250 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	251 @CMD_param_color@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	252 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	253 @CMD_pl_edges@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	254 arrows=$method.arrows,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	255 sort_order=$method.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	256 @CMD_params_groups@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	257 @CMD_params_pl_components@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	258 @CMD_pl_attribute_section@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	259 @CMD_params_matplotlib_pyplot_scatter@)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	260
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	261 #else if $method.method == 'pl.diffmap'
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	262 sc.pl.diffmap(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	263 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	264 @CMD_param_color@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	265 use_raw=$method.use_raw,
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	266 sort_order=$method.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	267 @CMD_params_groups@
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	268 @CMD_params_pl_components@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	269 @CMD_pl_attribute_section@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	270 @CMD_params_matplotlib_pyplot_scatter@)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	271
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	272 #else if $method.method == '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	273 sc.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	274 @CMD_param_plot_inputs@
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	275 @CMD_param_color@
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	276 #if $method.gene_symbols
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	277 gene_symbols='$method.gene_symbols',
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	278 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	279 use_raw=$method.use_raw,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	280 layout='$method.layout',
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	281 edges=$method.edges.edges,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	282 #if str($method.edges.edges) == 'True'
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	283 edges_width=$method.edges.edges_width,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	284 edges_color='$method.edges.edges_color',
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	285 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	286 arrows=$method.arrows,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	287 sort_order=$method.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	288 @CMD_params_groups@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	289 @CMD_params_pl_components@
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	290 @CMD_pl_attribute_section@
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	291 @CMD_params_matplotlib_pyplot_scatter@)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	292
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	293 #else if $method.method == 'pl.embedding_density'
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	294 sc.pl.embedding_density(
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	295 @CMD_param_plot_inputs@
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	296 basis='$method.basis',
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	297 #if $method.key
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	298 key='$method.key',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	299 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	300 #if $method.groupby
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	301 groupby='$method.groupby',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	302 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	303 #if $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	304 #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	305 group=$group,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	306 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	307 #if $method.color_map
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	308 color_map='$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	309 #end if
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	310 bg_dotsize=$method.bg_dotsize,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	311 fg_dotsize=$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	312 ncols=$method.ncols,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	313 wspace=$method.wspace,
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	314 hspace=$method.hspace)
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	315
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	316 #else if $method.method == '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	317 sc.pl.dpt_groups_pseudotime(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	318 @CMD_param_plot_inputs@
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	319 #if $method.color_map
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	320 color_map='$method.color_map'
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	321 #end if
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	322 )
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	323
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	324 #else if $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	325 sc.pl.dpt_timeseries(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	326 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	327 #if $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	328 #if $method.heatmap.color_map
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	329 color_map='$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	330 #end if
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	331 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	332 as_heatmap=$method.heatmap.as_heatmap)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	333
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	334 #else if $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	335 sc.pl.paga(
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	336 @CMD_param_plot_inputs@
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	337 @CMD_params_pl_paga@)
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	338
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	339 #else if $method.method == '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	340 sc.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	341 @CMD_param_plot_inputs@
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	342 @CMD_params_pl_paga@)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	343
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	344 #else if $method.method == '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	345 sc.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	346 @CMD_param_plot_inputs@
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	347 #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	348 nodes=$nodes,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	349 #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	350 keys=$keys,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	351 use_raw=$method.use_raw,
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	352 #if $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	353 #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	354 annotations=$annotations,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	355 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	356 #if $method.color_map
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	357 color_map='$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	358 #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	359 n_avg=$method.n_avg,
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	360 #if $method.annotations
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	361 groups_key='$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	362 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	363 as_heatmap=$method.as_heatmap,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	364 show_node_names=$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	365 show_colorbar=$method.show_colorbar,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	366 show_yticks=$method.show_yticks,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	367 normalize_to_zero_one=$method.normalize_to_zero_one)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	368
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	369 #else if $method.method == 'pl.rank_genes_groups'
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	370 sc.pl.rank_genes_groups(
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	371 @CMD_param_plot_inputs@
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	372 @CMD_params_groups@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	373 n_genes=$method.n_genes,
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	374 #if $method.gene_symbols
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	375 gene_symbols='$method.gene_symbols',
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	376 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	377 fontsize=$method.fontsize,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	378 ncols=$method.ncols,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	379 sharey=$method.sharey)
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	380
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	381 #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	382 sc.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	383 @CMD_param_plot_inputs@
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	384 @CMD_params_groups@
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	385 #if $method.genes.select == 'n_genes'
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	386 n_genes=$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	387 #else
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	388 #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	389 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	390 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	391 #if $method.gene_symbols
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	392 gene_symbols='$method.gene_symbols',
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	393 #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	394 use_raw=$method.use_raw,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	395 split=$method.split,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	396 strip=$method.violin_plot.stripplot.stripplot,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	397 #if $method.violin_plot.stripplot.stripplot == "True"
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	398 jitter=$method.violin_plot.stripplot.jitter.jitter,
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	399 #if $method.violin_plot.stripplot.jitter.jitter == "True"
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	400 size=$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	401 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	402 #end if
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	403 scale='$method.violin_plot.scale')
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	404
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	405 #else if $method.method == 'pl.rank_genes_groups_dotplot'
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	406
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	407 @CMD_var_names_header_check@
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	408
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	409 sc.pl.rank_genes_groups_dotplot(
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	410 @CMD_param_plot_inputs@
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	411 #if $method.var_names.type == 'custom'
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	412 #set $var_names = ([x.strip() for x in str($method.var_names.var_names).split(',')])
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	413 var_names=$var_names,
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	414 #else if $method.var_names.type == 'customfile'
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	415 var_names={key: [v for v in list(value.values()) if pd.notna(v)] for key, value in pd.read_csv('$var_names', sep='\t', index_col=0, header=header).to_dict(orient='index').items()},
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	416 #else
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	417 n_genes=$method.n_genes,
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	418 #end if
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	419 #if $method.groupby != ''
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	420 groupby='$method.groupby',
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	421 #end if
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	422 num_categories=$method.num_categories,
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	423 #if $method.key != ''
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	424 key='$method.key',
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	425 #end if
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	426 #if $method.gene_symbols
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	427 gene_symbols='$method.gene_symbols',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	428 #end if
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	429 @CMD_params_plots@
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	430 @CMD_pl_dotplot@)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	431
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	432 #else if $method.method == '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	433 sc.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	434 @CMD_param_plot_inputs@
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	435 @CMD_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	436 @CMD_params_plots@
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	437 #if $method.gene_symbols
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	438 gene_symbols='$method.gene_symbols',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	439 #end if
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	440 @CMD_pl_heatmap@)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	441
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	442 #else if $method.method == '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	443 sc.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	444 @CMD_param_plot_inputs@
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	445 @CMD_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	446 @CMD_params_plots@
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	447 #if $method.gene_symbols
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	448 gene_symbols='$method.gene_symbols',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	449 #end if
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	450 @CMD_pl_matrixplot@)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	451
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	452 #else if $method.method == 'pl.rank_genes_groups_stacked_violin'
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	453 sc.pl.rank_genes_groups_stacked_violin(
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	454 @CMD_param_plot_inputs@
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	455 @CMD_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	456 @CMD_params_plots@
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	457 #if $method.gene_symbols
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	458 gene_symbols='$method.gene_symbols',
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	459 #end if
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	460 @CMD_pl_stacked_violin@)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	461
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	462 #end if
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	463 ]]></configfile>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	464 </configfiles>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	465 <inputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	466 <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	467 <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	468 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	469 <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	470 <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	471 <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	472 <option value="pl.dotplot">Generic: Makes a dot plot of the expression values, using 'pl.dotplot'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	473 <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	474 <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	475 <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	476 <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	477 <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	478 <!--<option value="pl.filter_genes_dispersion">Preprocessing: Plot dispersions versus means for genes, using 'pl.filter_genes_dispersion'</option>-->
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	479 <option value="pl.highly_variable_genes">Preprocessing: Plot dispersions versus means for genes, using 'pl.highly_variable_genes'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	480 <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	481 <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	482 <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	483 <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	484 <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	485 <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	486 <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	487 <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	488 <option value="pl.embedding_density">Embeddings: Plot the density of cells in an embedding (per condition), using 'pl.embedding_density'</option>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	489 <option value="pl.dpt_groups_pseudotime">Branching trajectories and pseudotime, clustering: Plot groups and pseudotime, using 'pl.dpt_groups_pseudotime'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	490 <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	491 <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	492 <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	493 <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	494 <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	495 <option value="pl.rank_genes_groups_violin">Marker genes: Plot ranking of genes as violin plot, using 'pl.rank_genes_groups_violin'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	496 <option value="pl.rank_genes_groups_dotplot">Marker genes: Plot ranking of genes as dotplot plot, using 'pl.rank_genes_groups_dotplot'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	497 <option value="pl.rank_genes_groups_heatmap">Marker genes: Plot ranking of genes as heatmap plot, using 'pl.rank_genes_groups_heatmap'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	498 <option value="pl.rank_genes_groups_matrixplot">Marker genes: Plot ranking of genes as matrixplot plot, using 'pl.rank_genes_groups_matrixplot'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	499 <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>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	500 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	501 <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	502 <conditional name="type">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	503 <param name="type" type="select" label="Plotting tool that computed coordinates" help="">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	504 <option value="xy">Using coordinates</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	505 <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	506 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	507 <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	508 <param argument="x" type="text" value="" label="x coordinate" help="Index or key from either '.obs' or '.var'">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	509 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	510 </param>
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	511 <param argument="y" type="text" value="" label="y coordinate" help="Index or key from either '.obs' or '.var'">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	512 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	513 </param>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	514 <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	515 <param argument="color" type="text" value="" label="Color by" help="Color points by single variable in `.obs` or `.var`">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	516 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	517 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	518 <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	519 <param argument="use_layers" type="select" label="Use the layers attribute?">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	520 <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	521 <option value="false" selected="true">No</option>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	522 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	523 <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	524 <param argument="layer_x" type="text" value="" optional="true" label="Layers for x coordinate" help="Use the 'layers' attribute of 'adata' if present">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	525 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	526 </param>
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	527 <param argument="layer_y" type="text" value="" optional="true" label="Layers for y coordinate" help="Use the 'layers' attribute of 'adata' if present">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	528 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	529 </param>
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	530 <param argument="layer_color" type="text" value="" optional="true" label="Layers for color" help="Use the 'layers' attribute of 'adata' if present">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	531 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	532 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	533 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	534 <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	535 </conditional>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	536 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	537 <when value="basis">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	538 <param argument="basis" type="select" label="Plotting tool that computes coordinates" help="">
3 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="pca">pca (need to run on 'tl.pca' output)</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="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	541 <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	542 <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	543 <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	544 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	545 <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	546 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	547 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	548 <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	549 <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	550 <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	551 <section name="plot" title="Plot attributes">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	552 <expand macro="pl_components"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	553 <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	554 <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	555 <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	556 <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	557 <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	558 <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	559 <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	560 <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	561 <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	562 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	563 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	564 <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	565 <expand macro="params_inputs"/>
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	566 <expand macro="gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	567 <expand macro="params_plots"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	568 <expand macro="pl_heatmap"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	569 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	570 <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	571 <expand macro="params_inputs"/>
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	572 <expand macro="gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	573 <expand macro="params_plots"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	574 <expand macro="pl_dotplot"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	575 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	576 <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	577 <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	578 <param name="type" type="select" label="Keys for accessing variables">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	579 <option value="var_names">All variables in '.var_names'</option>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	580 <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	581 <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	582 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	583 <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	584 <when value="obs"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	585 <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	586 <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'">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	587 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	588 </param>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	589 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	590 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	591 <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	592 <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	593 <expand macro="param_use_raw"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	594 <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	595 <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	596 <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	597 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when 'groupby is not provided">
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	598 <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	599 <option value="False" selected="true">No</option>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	600 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	601 <when value="True">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	602 <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure" help=""/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	603 <param argument="height" type="integer" min="0" value="" optional="true" label="Height of the figure" help=""/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	604 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	605 <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	606 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	607 <expand macro="param_scale"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	608 </section>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	609 <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.">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	610 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	611 </param>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	612 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	613 <expand macro="seaborn_violinplot"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	614 </when>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	615 <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	616 <expand macro="params_inputs"/>
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	617 <expand macro="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	618 <expand macro="params_plots"/>
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="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	620 </when>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	621 <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	622 <expand macro="params_inputs"/>
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	623 <expand macro="gene_symbols"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	624 <expand macro="params_plots"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	625 <expand macro="pl_matrixplot"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	626 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	627 <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	628 <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.">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	629 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	630 </param>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	631 <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	632 <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	633 <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">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	634 <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	635 <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	636 <option value="average">average: UPGMA algorithm</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	637 <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	638 <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	639 <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	640 <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	641 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	642 <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	643 <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	644 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	645 <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.">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	646 <option value="None">No Z-score</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	647 <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	648 <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	649 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	650 <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.">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	651 <option value="None">No standardization</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	652 <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	653 <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	654 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	655 <param name="col_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the columns?" help=""/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	656 <param name="row_cluster" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Cluster the rows?" help=""/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	657 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	658 </when>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	659 <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	660 <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	661 <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	662 </when>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	663 <when value="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	664 <param argument="n_top" type="integer" min="0" value="30" label="Number of top genes" help=""/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	665 <param argument="gene_symbols" type="text" optional="true" label="Key for field in '.var' that stores gene symbols" help="Fill it if you do not want to use '.var_names'.">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	666 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	667 </param>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	668 <section name="setseaborn_boxplot" title="Plot settings" expanded="false">
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	669 <param argument="color" type="text" value="" optional="true" label="Color for all of the elements, or seed for a gradient palette" help="">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	670 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	671 </param>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	672 <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.">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	673 <expand macro="seaborn_color_palette_options"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	674 </param>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	675 <param argument="saturation" type="float" value="1" 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	676 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	677 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	678 <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	679 <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	680 <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	681 <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	682 <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	683 <expand macro="pl_attribute_section"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	684 <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	685 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	686 <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	687 <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">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	688 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	689 </param>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	690 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	691 <when 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	692 <param argument="n_pcs" type="integer" min="0" value="30" label="Number of PCs to show" help=""/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	693 <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	694 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	695 <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	696 <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	697 <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	698 <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	699 <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	700 <expand macro="pl_attribute_section"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	701 <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	702 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	703 <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	704 <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	705 <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	706 <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	707 <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	708 <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	709 <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	710 <expand macro="pl_attribute_section"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	711 <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	712 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	713 <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	714 <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	715 <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	716 <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	717 <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	718 <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	719 <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	720 <expand macro="pl_attribute_section"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	721 <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	722 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	723 <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	724 <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	725 <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	726 <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	727 <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	728 <expand macro="pl_attribute_section"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	729 <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	730 </when>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	731 <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	732 <expand macro="param_color"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	733 <expand macro="gene_symbols"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	734 <expand macro="param_use_raw"/>
8 6adf98e782f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec" iuc parents: 7 diff changeset	735 <param argument="layout" type="select" optional="false" label="Plotting layout" help="">
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	736 <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	737 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	738 <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	739 <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	740 <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	741 <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	742 <expand macro="pl_attribute_section"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	743 <expand macro="section_matplotlib_pyplot_scatter"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	744 </when>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	745 <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	746 <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]']">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	747 <expand macro="sanitize_query" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	748 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	749 <param argument="key" type="text" optional="true" value="" label="Name of the .obs covariate that contains the density estimates" help="Alternatively, pass _groupby_.">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	750 <expand macro="sanitize_query" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	751 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	752 <param argument="groupby" type="text" optional="true" value="" label="Name of the condition used in tl.embedding_density" help="Alternatively, pass _key_.">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	753 <expand macro="sanitize_query" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	754 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	755 <param argument="group" type="text" optional="all" value="" label="The category in the categorical observation annotation to be plotted"
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	756 help="For example, 'G1' in the cell cycle 'phase' covariate. If multiple categories want to be plotted use a comma separated list">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	757 <expand macro="sanitize_query" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	758 </param>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	759 <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	760 <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	761 <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	762 <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	763 <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	764 <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	765 </when>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	766 <when value="pl.dpt_groups_pseudotime">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	767 <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	768 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	769 <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	770 <conditional name="heatmap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	771 <param argument="as_heatmap" type="select" label="Plot the timeseries as heatmap?" help="">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	772 <option value="True">Yes</option>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	773 <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	774 </param>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	775 <when value="True">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	776 <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	777 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	778 <when value="False" />
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	779 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	780 </when>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	781 <when value="pl.paga">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	782 <expand macro="inputs_paga"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	783 </when>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	784 <when value="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	785 <expand macro="inputs_paga"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	786 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	787 <when value="pl.paga_path">
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	788 <param argument="nodes" type="text" value="" label="A path through nodes of the abstracted graph"
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	789 help="Each node is represented by its indice (within .categories) for the groups that have been used to run PAGA. Comma-separated">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	790 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	791 </param>
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	792 <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'">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	793 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	794 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	795 <expand macro="param_use_raw"/>
7 7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	796 <param argument="annotations" type="text" value="" optional="true" label="Key to plot" help="Keys for obs, comma-separated">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	797 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	798 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	799 <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	800 <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	801 <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">
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	802 <expand macro="sanitize_query" />
7647e5cd1b8b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 150c96596b94f9658c8b7c44814c420d38fbee0c" iuc parents: 6 diff changeset	803 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	804 <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	805 <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	806 <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	807 <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	808 <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	809 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	810 <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	811 <expand macro="param_groups"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	812 <expand macro="param_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	813 <expand macro="gene_symbols"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	814 <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	815 <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	816 <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	817 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	818 <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	819 <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	820 <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	821 <param argument="select" type="select" label="Which genes to plot?" help="">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	822 <option value="n_genes">A number 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	823 <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	824 </param>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	825 <when value="n_genes">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	826 <expand macro="param_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	827 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	828 <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	829 <param argument="gene_names" type="text" value="" label="List of genes to plot" help="A list of comma-separated names">
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	830 <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	831 </param>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	832 </when>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	833 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	834 <expand macro="gene_symbols"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	835 <expand macro="param_use_raw"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	836 <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	837 <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	838 <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	839 <expand macro="param_scale"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	840 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	841 </when>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	842 <when value="pl.rank_genes_groups_dotplot">
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	843 <expand macro="params_inputs"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	844 <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	845 <expand macro="params_plots"/>
11 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="gene_symbols"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	847 <expand macro="pl_dotplot"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	848 </when>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	849 <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	850 <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	851 <expand macro="params_plots"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	852 <expand macro="gene_symbols"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	853 <expand macro="pl_heatmap"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	854 </when>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	855 <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	856 <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	857 <expand macro="params_plots"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	858 <expand macro="gene_symbols"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	859 <expand macro="pl_matrixplot"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	860 </when>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	861 <when value="pl.rank_genes_groups_stacked_violin">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	862 <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	863 <expand macro="params_plots"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	864 <expand macro="gene_symbols"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	865 <expand macro="pl_stacked_violin"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	866 </when>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	867 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	868 <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	869 </inputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	870 <outputs>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	871 <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	872 <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	873 </data>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	874 <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	875 <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	876 <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	877 </collection>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	878 <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	879 <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	880 </data>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	881 <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	882 <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	883 <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	884 </collection>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	885 <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	886 <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	887 </data>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	888 <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	889 <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	890 <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	891 </collection>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	892 <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	893 <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	894 </data>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	895 </outputs>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	896 <tests>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	897 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	898 <!-- test 1: pl.scatter -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	899 <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	900 <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	901 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	902 <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	903 <conditional name="type">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	904 <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	905 <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	906 <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	907 </conditional>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	908 <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	909 <param name="sort_order" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	910 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	911 <param name="projection" value="2d"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	912 <param name="legend_loc" value="right margin"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	913 <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	914 <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	915 <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	916 <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	917 <param name="frameon" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	918 <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	919 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	920 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	921 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	922 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	923 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	924 <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	925 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	926 <has_text_matching expression="sc.pl.scatter"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	927 <has_text_matching expression="basis='umap'" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	928 <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	929 <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	930 <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	931 <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	932 <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	933 <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	934 <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	935 <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	936 <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	937 <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	938 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	939 </output>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	940 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	941 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	942 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	943 <!-- test 2: pl.scatter -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	944 <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	945 <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	946 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	947 <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	948 <conditional name="type">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	949 <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	950 <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	951 <param name="y" value="Cebpa"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	952 <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	953 <param name="use_layers" value="false"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	954 </conditional>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	955 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	956 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	957 <param name="sort_order" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	958 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	959 <param name="projection" value="2d"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	960 <param name="legend_loc" value="right margin"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	961 <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	962 <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	963 <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	964 <param name="frameon" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	965 <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	966 <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	967 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	968 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	969 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	970 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	971 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	972 <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	973 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	974 <has_text_matching expression="sc.pl.scatter"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	975 <has_text_matching expression="x_field='EKLF'" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	976 <has_text_matching expression="y_field='Cebpa'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	977 <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	978 <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	979 <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	980 <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	981 <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	982 <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	983 <has_text_matching expression="frameon=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	984 <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	985 <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	986 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	987 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	988 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	989 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	990 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	991 <!-- test 3: pl.heatmap -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	992 <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	993 <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	994 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	995 <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	996 <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	997 <param name="type" value="all"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	998 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	999 <param name="groupby" value="cell_type"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	1000 <param name="num_categories" value="7"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1001 <param name="log" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1002 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1003 <conditional name="figsize">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1004 <param name="test" value="yes"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1005 <param name="width" value="10" />
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1006 <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	1007 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1008 <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	1009 <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	1010 <param name="show_gene_labels" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1011 <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	1012 <param name="cmap" value="YlGnBu"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1013 <param name="interpolation" value="None"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1014 <param name="origin" value="upper"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1015 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1016 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1017 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1018 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1019 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1020 <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	1021 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1022 <has_text_matching expression="sc.pl.heatmap"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1023 <has_text_matching expression="var_names=adata.var_names" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1024 <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	1025 <has_text_matching expression="log=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1026 <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	1027 <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	1028 <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	1029 <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	1030 <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	1031 <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	1032 <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	1033 <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	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 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1036 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1037 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1038 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1039 <!-- test 4: pl.heatmap with symbols -->
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1040 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1041 <param name="format" value="png"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1042 <conditional name="method">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1043 <param name="method" value="pl.heatmap"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1044 <conditional name="var_names">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1045 <param name="type" value="custom"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1046 <param name="var_names" value="Fog1,EKLF,SCL"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1047 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1048 <param name="groupby" value="cell_type"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1049 <param name="gene_symbols" value="symbol"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1050 <param name="num_categories" value="7"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1051 <param name="log" value="False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1052 <param name="use_raw" value="False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1053 <conditional name="figsize">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1054 <param name="test" value="yes"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1055 <param name="width" value="10" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1056 <param name="height" value="3"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1057 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1058 <param name="dendrogram" value="True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1059 <param name="swap_axes" value="True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1060 <param name="show_gene_labels" value="True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1061 <section name="matplotlib_pyplot_imshow">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1062 <param name="cmap" value="YlGnBu"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1063 <param name="interpolation" value="None"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1064 <param name="origin" value="upper"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1065 </section>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1066 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1067 <section name="advanced_common">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1068 <param name="show_log" value="true" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1069 </section>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1070 <output name="hidden_output">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1071 <assert_contents>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1072 <has_text_matching expression="sc.pl.heatmap"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1073 <has_text_matching expression="gene_symbols='symbol'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1074 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1075 <has_text_matching expression="groupby='cell_type'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1076 <has_text_matching expression="log=False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1077 <has_text_matching expression="use_raw=False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1078 <has_text_matching expression="num_categories=7"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1079 <has_text_matching expression="dendrogram=True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1080 <has_text_matching expression="figsize=$10, 3$"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1081 <has_text_matching expression="swap_axes=True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1082 <has_text_matching expression="show_gene_labels=True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1083 <has_text_matching expression="cmap='YlGnBu'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1084 <has_text_matching expression="origin='upper'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1085 </assert_contents>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1086 </output>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1087 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1088 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1089 <!-- test 5: pl.dotplot -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1090 <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	1091 <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	1092 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1093 <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	1094 <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	1095 <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	1096 <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	1097 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1098 <param name="groupby" value="louvain"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	1099 <param name="num_categories" value="7"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1100 <param name="log" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1101 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1102 <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	1103 <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	1104 <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	1105 <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	1106 <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	1107 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1108 <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	1109 <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	1110 <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	1111 <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	1112 </repeat>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1113 <conditional name="figsize">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1114 <param name="test" value="no"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1115 </conditional>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1116 <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	1117 <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	1118 <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	1119 <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	1120 <param name="linewidths" value="0" />
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1121 <param name="edgecolors" value="face"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1122 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1123 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1124 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1125 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1126 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1127 <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	1128 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1129 <has_text_matching expression="sc.pl.dotplot"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1130 <has_text_matching expression="var_names=\['CD79A', 'MS4A1', 'CD8A', 'CD8B', 'LYZ', 'GNLY', 'NKG7', 'RP3-467N11.1', 'FCGR3A', 'FCER1A', 'CST3', 'POU2AF1', 'LINC00402'\]" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1131 <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	1132 <has_text_matching expression="log=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1133 <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	1134 <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	1135 <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	1136 <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	1137 <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	1138 <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	1139 <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	1140 <has_text_matching expression="dot_min=0.1"/>
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1141 <has_text_matching expression="lw=0.0"/>
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1142 <has_text_matching expression="ec='face'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1143 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1144 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1145 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1146 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1147 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1148 <!-- test 6: pl.dotplot with symbols -->
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1149 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1150 <param name="format" value="png"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1151 <conditional name="method">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1152 <param name="method" value="pl.dotplot"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1153 <conditional name="var_names">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1154 <param name="type" value="custom"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1155 <param name="var_names" value="Fog1,EKLF,SCL"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1156 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1157 <param name="groupby" value="cell_type"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1158 <param name="gene_symbols" value="symbol"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1159 <param name="num_categories" value="7"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1160 <param name="log" value="False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1161 <param name="use_raw" value="False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1162 <param name="dendrogram" value="True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1163 <section name="matplotlib_pyplot_imshow">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1164 <param name="cmap" value="YlGnBu"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1165 <param name="interpolation" value="None"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1166 <param name="origin" value="upper"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1167 </section>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1168 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1169 <section name="advanced_common">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1170 <param name="show_log" value="true" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1171 </section>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1172 <output name="hidden_output">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1173 <assert_contents>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1174 <has_text_matching expression="sc.pl.dotplot"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1175 <has_text_matching expression="gene_symbols='symbol'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1176 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1177 <has_text_matching expression="groupby='cell_type'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1178 <has_text_matching expression="log=False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1179 <has_text_matching expression="use_raw=False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1180 <has_text_matching expression="num_categories=7"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1181 <has_text_matching expression="dendrogram=True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1182 </assert_contents>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1183 </output>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1184 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1185 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1186 <!-- test 7: pl.violin -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1187 <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	1188 <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	1189 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1190 <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	1191 <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	1192 <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	1193 <param name="keys" value="n_genes, percent_mito, n_counts" />
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1194 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1195 <param name="log" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1196 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1197 <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	1198 <conditional name="stripplot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1199 <param name="stripplot" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1200 <param name="jitter" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1201 <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	1202 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1203 <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	1204 <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	1205 <param name="width" value="20"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1206 <param name="height" value="20"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1207 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1208 <param name="scale" value="width"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1209 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1210 <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	1211 <param name="bw" value="scott"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1212 <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	1213 <param name="color" value="AliceBlue"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1214 <param name="palette" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1215 <param name="saturation" value="0.75"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1216 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1217 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1218 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1219 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1220 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1221 <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	1222 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1223 <has_text_matching expression="sc.pl.violin"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1224 <has_text_matching expression="keys=\['n_genes', 'percent_mito', 'n_counts'\]" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1225 <has_text_matching expression="log=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1226 <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	1227 <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	1228 <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	1229 <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	1230 <has_text_matching expression="multi_panel=True"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1231 <has_text_matching expression="figsize=$20, 20$"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1232 <has_text_matching expression="scale='width'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1233 <has_text_matching expression="bw='scott'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1234 <has_text_matching expression="scale='width'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1235 <has_text_matching expression="linewidth=0.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1236 <has_text_matching expression="color='AliceBlue'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1237 <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	1238 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1239 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1240 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1241 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1242 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1243 <!-- test 8: 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	1244 <param name="adata" value="krumsiek11.h5ad" />
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1245 <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	1246 <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	1247 <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	1248 <conditional name="var_names">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1249 <param name="type" value="all"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1250 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1251 <param name="groupby" value="cell_type"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	1252 <param name="num_categories" value="7"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1253 <param name="log" value="False"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1254 <param name="use_raw" value="False"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1255 <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	1256 <conditional name="figsize">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1257 <param name="test" value="no"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1258 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1259 <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	1260 <section name="violin_plot">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1261 <conditional name="stripplot">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1262 <param name="stripplot" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1263 <param name="jitter" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1264 <param name="size" value="1"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1265 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1266 <param name="scale" value="width"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1267 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1268 <param name="row_palette" value="muted"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1269 <param name="standard_scale" value="None"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1270 <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	1271 <param name="bw" value="scott"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1272 <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	1273 <param name="color" value="AliceBlue"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1274 <param name="saturation" value="0.75"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1275 </section>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1276 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1277 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1278 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1279 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1280 <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	1281 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1282 <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	1283 <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	1284 <has_text_matching expression="log=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1285 <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	1286 <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	1287 <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	1288 <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	1289 <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	1290 <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	1291 <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	1292 <has_text_matching expression="scale='width'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1293 <has_text_matching expression="bw='scott'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1294 <has_text_matching expression="scale='width'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1295 <has_text_matching expression="linewidth=0.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1296 <has_text_matching expression="color='AliceBlue'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1297 <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	1298 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1299 </output>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1300 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1301 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1302 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1303 <!-- test 9: pl.stacked_violin with symbols -->
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1304 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1305 <param name="format" value="png"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1306 <conditional name="method">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1307 <param name="method" value="pl.stacked_violin"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1308 <conditional name="var_names">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1309 <param name="type" value="custom"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1310 <param name="var_names" value="Fog1,EKLF,SCL"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1311 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1312 <param name="groupby" value="cell_type"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1313 <param name="gene_symbols" value="symbol"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1314 <param name="num_categories" value="7"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1315 <param name="log" value="False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1316 <param name="use_raw" value="False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1317 <param name="dendrogram" value="True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1318 <param name="swap_axes" value="True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1319 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1320 <section name="advanced_common">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1321 <param name="show_log" value="true" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1322 </section>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1323 <output name="hidden_output">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1324 <assert_contents>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1325 <has_text_matching expression="sc.pl.stacked_violin"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1326 <has_text_matching expression="gene_symbols='symbol'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1327 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1328 <has_text_matching expression="groupby='cell_type'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1329 <has_text_matching expression="log=False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1330 <has_text_matching expression="use_raw=False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1331 <has_text_matching expression="num_categories=7"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1332 <has_text_matching expression="dendrogram=True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1333 <has_text_matching expression="swap_axes=True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1334 </assert_contents>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1335 </output>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1336 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1337 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1338 <!-- test 10: pl.matrixplot -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1339 <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	1340 <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	1341 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1342 <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	1343 <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	1344 <param name="type" value="all"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1345 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1346 <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	1347 <param name="log" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1348 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1349 <param name="num_categories" value="7"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1350 <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	1351 <conditional name="figsize">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1352 <param name="test" value="no"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1353 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1354 <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	1355 <section name="matplotlib_pyplot_pcolor">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1356 <param name="cmap" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1357 <param name="edgecolors" value="face"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1358 <param name="snap" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1359 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1360 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1361 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1362 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1363 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1364 <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	1365 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1366 <has_text_matching expression="sc.pl.matrixplot"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1367 <has_text_matching expression="var_names=adata.var_names" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1368 <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	1369 <has_text_matching expression="log=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1370 <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	1371 <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	1372 <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	1373 <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	1374 <has_text_matching expression="cmap='viridis'"/>
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1375 <has_text_matching expression="ec='face'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1376 <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	1377 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1378 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1379 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1380 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1381 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1382 <!-- test 11: pl.matrixplot with symbols -->
9 9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1383 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1384 <param name="format" value="png"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1385 <conditional name="method">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1386 <param name="method" value="pl.matrixplot"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1387 <conditional name="var_names">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1388 <param name="type" value="custom"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1389 <param name="var_names" value="Fog1,EKLF,SCL"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1390 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1391 <param name="groupby" value="cell_type"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1392 <param name="gene_symbols" value="symbol"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1393 <param name="num_categories" value="7"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1394 <param name="log" value="False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1395 <param name="use_raw" value="False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1396 <conditional name="figsize">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1397 <param name="test" value="yes"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1398 <param name="width" value="10" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1399 <param name="height" value="3"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1400 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1401 <param name="dendrogram" value="True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1402 <param name="swap_axes" value="False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1403 </conditional>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1404 <section name="advanced_common">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1405 <param name="show_log" value="true" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1406 </section>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1407 <output name="hidden_output">
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1408 <assert_contents>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1409 <has_text_matching expression="sc.pl.matrixplot"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1410 <has_text_matching expression="gene_symbols='symbol'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1411 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1412 <has_text_matching expression="groupby='cell_type'"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1413 <has_text_matching expression="log=False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1414 <has_text_matching expression="use_raw=False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1415 <has_text_matching expression="num_categories=7"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1416 <has_text_matching expression="dendrogram=True"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1417 <has_text_matching expression="swap_axes=False"/>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1418 </assert_contents>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1419 </output>
9a169729c9f9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927" iuc parents: 8 diff changeset	1420 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1421 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1422 <!-- test 12: pl.clustermap -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1423 <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	1424 <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	1425 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1426 <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	1427 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1428 <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	1429 <param name="method" value="single"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1430 <param name="metric" value="euclidean"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1431 <param name="z_score" value="None"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1432 <param name="standard_scale" value="None"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1433 <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	1434 <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	1435 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1436 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1437 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1438 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1439 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1440 <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	1441 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1442 <has_text_matching expression="sc.pl.clustermap"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1443 <has_text_matching expression="adata=adata" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1444 <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	1445 <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	1446 <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	1447 <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	1448 <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	1449 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1450 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1451 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1452 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1453 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1454 <!-- test 13: pl.highest_expr_genes -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1455 <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	1456 <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	1457 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1458 <param name="method" value="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	1459 <param name="n_top" value="30"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1460 <param name="gene_symbols" value="means"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1461 <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	1462 <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	1463 <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	1464 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1465 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1466 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1467 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1468 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1469 <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	1470 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1471 <has_text_matching expression="sc.pl.highest_expr_genes"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1472 <has_text_matching expression="n_top=30" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1473 <has_text_matching expression="gene_symbols='means'" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1474 <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	1475 <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	1476 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1477 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1478 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1479 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1480 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1481 <!-- test 14: 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	1482 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad" />
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1483 <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	1484 <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	1485 <param name="method" 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	1486 <param name="log" value="false"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1487 <param name="highly_variable_genes" value="true"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1488 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1489 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1490 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1491 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1492 <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	1493 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1494 <has_text_matching expression="sc.pl.highly_variable_genes"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1495 <has_text_matching expression="adata_or_result=adata" />
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="log=False" />
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="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	1498 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1499 </output>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1500 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="sim_size"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1501 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1502 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1503 <!-- test 15: pl.pca -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1504 <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	1505 <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	1506 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1507 <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	1508 <param name="color" value="CD3D,CD79A"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1509 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1510 <param name="sort_order" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1511 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1512 <repeat name="components">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1513 <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	1514 <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	1515 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1516 <repeat name="components">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1517 <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	1518 <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	1519 </repeat>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1520 <param name="projection" value="2d"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1521 <param name="legend_loc" value="right margin"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1522 <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	1523 <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	1524 <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	1525 <param name="palette" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1526 <param name="frameon" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1527 <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	1528 <param name="wspace" value="0.1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1529 <param name="hspace" value="0.25"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1530 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1531 <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	1532 <param name="linewidths" value="0"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1533 <param name="edgecolors" value="face"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1534 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1535 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1536 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1537 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1538 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1539 <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	1540 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1541 <has_text_matching expression="sc.pl.pca"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1542 <has_text_matching expression="save='.pdf'" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1543 <has_text_matching expression="color=\['CD3D', 'CD79A'\]" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1544 <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	1545 <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	1546 <has_text_matching expression="components=\['1,2', '1,3'\]" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1547 <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	1548 <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	1549 <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	1550 <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	1551 <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	1552 <has_text_matching expression="palette='viridis'" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1553 <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	1554 <has_text_matching expression="ncols=2" />
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="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	1556 <has_text_matching expression="hspace=0.25" />
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1557 <has_text_matching expression="lw=0.0" />
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1558 <has_text_matching expression="ec='face'" />
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1559 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1560 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1561 <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	1562 </test>
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">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1564 <!-- test 16: pl.pca_loadings -->
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="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	1566 <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	1567 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1568 <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	1569 <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	1570 </conditional>
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 name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1572 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1573 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1574 <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	1575 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1576 <has_text_matching expression="sc.pl.pca_loadings"/>
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="components=\[1, 2, 3\]" />
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>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1580 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="sim_size"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1581 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1582 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1583 <!-- test 17: pl.pca_variance_ratio -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1584 <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	1585 <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	1586 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1587 <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	1588 <param name="n_pcs" value="5"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1589 <param name="log" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1590 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1591 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1592 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1593 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1594 <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	1595 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1596 <has_text_matching expression="sc.pl.pca_variance_ratio"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1597 <has_text_matching expression="n_pcs=5" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1598 <has_text_matching expression="log=False" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1599 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1600 </output>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1601 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="sim_size"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1602 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1603 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1604 <!-- test 18: pl.pca_overview -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1605 <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	1606 <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	1607 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1608 <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	1609 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1610 <param name="sort_order" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1611 <section name="plot">
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1612 <param name="projection" value="2d"/>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1613 <param name="legend_loc" value="right margin"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1614 <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	1615 <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	1616 <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	1617 <param name="palette" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1618 <param name="frameon" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1619 <param name="ncols" value="4"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1620 <param name="wspace" value="0.1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1621 <param name="hspace" value="0.25"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1622 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1623 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1624 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1625 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1626 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1627 <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	1628 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1629 <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	1630 <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	1631 <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	1632 <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	1633 <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	1634 <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	1635 <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	1636 <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	1637 <has_text_matching expression="palette='viridis'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1638 <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	1639 <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	1640 <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	1641 <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	1642 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1643 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1644 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1645 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1646 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1647 <!-- test 19: pl.tsne -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1648 <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	1649 <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	1650 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1651 <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	1652 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1653 <conditional name="edges">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1654 <param name="edges" value="False" />
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1655 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1656 <param name="arrows" value="False" />
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1657 <param name="sort_order" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1658 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1659 <param name="projection" value="2d"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1660 <param name="legend_loc" value="right margin"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1661 <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	1662 <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	1663 <param name="palette" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1664 <param name="frameon" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1665 <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	1666 <param name="ncols" value="4"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1667 <param name="wspace" value="0.1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1668 <param name="hspace" value="0.25"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1669 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1670 <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	1671 <param name="linewidths" value="0"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1672 <param name="edgecolors" value="face"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1673 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1674 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1675 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1676 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1677 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1678 <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	1679 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1680 <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	1681 <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	1682 <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	1683 <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	1684 <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	1685 <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	1686 <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	1687 <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	1688 <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	1689 <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	1690 <has_text_matching expression="palette='viridis'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1691 <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	1692 <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	1693 <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	1694 <has_text_matching expression="hspace=0.25"/>
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1695 <has_text_matching expression="lw=0.0"/>
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1696 <has_text_matching expression="ec='face'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1697 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1698 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1699 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1700 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1701 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1702 <!-- test 20: pl.umap -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1703 <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	1704 <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	1705 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1706 <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	1707 <param name="color" value="paul15_clusters"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1708 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1709 <conditional name="edges">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1710 <param name="edges" value="True" />
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1711 <param name="edges_width" value="0.1" />
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1712 <param name="edges_color" value="AliceBlue"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1713 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1714 <param name="arrows" value="False" />
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1715 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1716 <param name="projection" value="2d"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1717 <param name="legend_loc" value="right margin"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1718 <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	1719 <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	1720 <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	1721 <param name="palette" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1722 <param name="frameon" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1723 <param name="ncols" value="4"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1724 <param name="wspace" value="0.1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1725 <param name="hspace" value="0.25"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1726 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1727 <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	1728 <param name="linewidths" value="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="edgecolors" value="face"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1730 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1731 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1732 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1733 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1734 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1735 <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	1736 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1737 <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	1738 <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	1739 <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	1740 <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	1741 <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	1742 <has_text_matching expression="edges_color='AliceBlue'"/>
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="arrows=False"/>
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="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	1745 <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	1746 <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	1747 <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	1748 <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	1749 <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	1750 <has_text_matching expression="palette='viridis'"/>
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="frameon=True"/>
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="ncols=4"/>
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="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	1754 <has_text_matching expression="hspace=0.25"/>
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1755 <has_text_matching expression="lw=0.0"/>
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1756 <has_text_matching expression="ec='face'"/>
6 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>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1759 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1760 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1761 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1762 <!-- test 21: pl.diffmap -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1763 <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	1764 <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	1765 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1766 <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	1767 <param name="color" value="paul15_clusters"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1768 <param name="use_raw" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1769 <param name="sort_order" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1770 <section name="plot">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1771 <param name="projection" value="2d"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1772 <param name="legend_loc" value="right margin"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1773 <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	1774 <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	1775 <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	1776 <param name="palette" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1777 <param name="frameon" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1778 <param name="ncols" value="4"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1779 <param name="wspace" value="0.1"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1780 <param name="hspace" value="0.25"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1781 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1782 <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	1783 <param name="linewidths" value="0"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1784 <param name="edgecolors" value="face"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1785 </section>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1786 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1787 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1788 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1789 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1790 <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	1791 <assert_contents>
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="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	1793 <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	1794 <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	1795 <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	1796 <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	1797 <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	1798 <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	1799 <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	1800 <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	1801 <has_text_matching expression="palette='viridis'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1802 <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	1803 <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	1804 <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	1805 <has_text_matching expression="hspace=0.25"/>
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1806 <has_text_matching expression="lw=0.0"/>
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1807 <has_text_matching expression="ec='face'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1808 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1809 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1810 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1811 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1812 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1813 <!-- test 22: 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	1814 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad" />
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1815 <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	1816 <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	1817 <param name="method" 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	1818 <param name="use_raw" value="false"/>
8 6adf98e782f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec" iuc parents: 7 diff changeset	1819 <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	1820 <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	1821 <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	1822 <param name="edges_width" value="0.1"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1823 <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	1824 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1825 <param name="arrows" value="false"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1826 <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	1827 <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	1828 <param name="projection" value="2d"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1829 <param name="legend_loc" value="right margin"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1830 <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	1831 <param name="palette" value="viridis"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1832 <param name="frameon" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1833 <param name="ncols" value="4"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1834 <param name="wspace" value="0.1"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1835 <param name="hspace" value="0.25"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1836 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1837 <section name="matplotlib_pyplot_scatter">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1838 <param name="linewidths" value="0"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1839 <param name="edgecolors" value="face"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1840 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1841 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1842 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1843 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1844 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1845 <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	1846 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1847 <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	1848 <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	1849 <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	1850 <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	1851 <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	1852 <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	1853 <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	1854 <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	1855 <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	1856 <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	1857 <has_text_matching expression="palette='viridis'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1858 <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	1859 <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	1860 <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	1861 <has_text_matching expression="hspace=0.25"/>
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1862 <has_text_matching expression="lw=0.0"/>
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	1863 <has_text_matching expression="ec='face"/>
6 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 </output>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1866 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="sim_size"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1867 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1868 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1869 <!-- test 23: 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	1870 <param name="adata" value="tl.embedding_density.umap.pbmc68k_reduced.h5ad" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1871 <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	1872 <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	1873 <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	1874 <param name="basis" value="umap"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1875 <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	1876 </conditional>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1877 <section name="advanced_common">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1878 <param name="show_log" value="true" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1879 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1880 <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	1881 <assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1882 <has_text_matching expression="sc.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	1883 <has_text_matching expression="basis='umap'" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1884 <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	1885 </assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1886 </output>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1887 <output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1888 </test>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1889 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1890 <!-- test 24: pl.dpt_groups_pseudotime -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1891 <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	1892 <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	1893 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1894 <param name="method" value="pl.dpt_groups_pseudotime"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1895 <param name="color_map" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1896 </conditional>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1897 <section name="advanced_common">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1898 <param name="show_log" value="true" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1899 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1900 <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	1901 <assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1902 <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	1903 <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	1904 </assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1905 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1906 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1907 </test>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1908 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1909 <!-- test 25: pl.dpt_timeseries -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1910 <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	1911 <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	1912 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1913 <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	1914 <conditional name="heatmap">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1915 <param name="as_heatmap" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1916 <param name="color_map" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1917 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1918 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1919 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1920 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1921 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1922 <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	1923 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1924 <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	1925 <has_text_matching expression="color_map='viridis'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1926 <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	1927 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1928 </output>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1929 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="sim_size"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1930 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1931 <test expect_num_outputs="1">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1932 <!-- test 26: pl.paga -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1933 <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	1934 <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	1935 <conditional name="method">
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1936 <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	1937 <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	1938 <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	1939 <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	1940 <param name="random_state" value="0"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1941 <param name="solid_edges" value="connectivities"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1942 <param name="single_component" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1943 <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	1944 <param name="node_size_scale" value="1.0"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1945 <param name="node_size_power" value="0.5"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1946 <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	1947 <param name="arrowsize" value="30"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1948 <param name="normalize_to_color" value="False"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1949 <param name="cmap" value="viridis"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1950 <param name="frameon" value="True"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1951 </conditional>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	1952 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1953 </test>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1954 <test expect_num_outputs="1">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1955 <!-- test 27: 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	1956 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1957 <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	1958 <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	1959 <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	1960 <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	1961 <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	1962 <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	1963 <param name="random_state" value="0"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1964 <param name="solid_edges" value="connectivities"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1965 <param name="single_component" value="False"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1966 <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	1967 <param name="node_size_scale" value="1.0"/>
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="node_size_power" value="0.5"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1969 <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	1970 <param name="arrowsize" value="30"/>
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="normalize_to_color" value="False"/>
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="cmap" value="viridis"/>
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="frameon" value="True"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1974 </conditional>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1975 <output name="out_png" file="pl.paga_compare.paul15_gauss_braycurtis.png" ftype="png" compare="sim_size"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1976 </test>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1977 <!--<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	1978 test pl.paga_path
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1979 </test>-->
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1980 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1981 <!-- test 28: 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	1982 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1983 <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	1984 <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	1985 <param name="method" value="pl.rank_genes_groups"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	1986 <param name="gene_symbols" value="symbol"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1987 <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	1988 <param name="fontsize" value="8"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1989 <param name="ncols" value="4"/>
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="sharey" value="true"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	1991 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1992 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1993 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1994 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1995 <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	1996 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	1997 <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	1998 <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	1999 <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	2000 <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	2001 <has_text_matching expression="sharey=True"/>
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>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2004 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2005 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2006 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2007 <!-- test 29: pl.rank_genes_groups_violin -->
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2008 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2009 <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	2010 <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	2011 <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	2012 <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	2013 <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	2014 <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	2015 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2016 <param name="use_raw" value="false"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2017 <param name="split" value="true"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2018 <section name="violin_plot">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2019 <conditional name="stripplot">
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2020 <param name="stripplot" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2021 <param name="jitter" value="True"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2022 <param name="size" value="1"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2023 </conditional>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2024 <param name="scale" value="width"/>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2025 </section>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2026 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2027 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2028 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2029 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2030 <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	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 <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	2033 <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	2034 <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	2035 <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	2036 <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	2037 <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	2038 <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	2039 <has_text_matching expression="scale='width'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2040 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2041 </output>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2042 <output_collection name="collection_png">
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2043 <element name="cell_type_Ery" file="pl.rank_genes_groups_violin.Ery.png" ftype="png" compare="sim_size"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2044 <element name="cell_type_Mk" file="pl.rank_genes_groups_violin.Mk.png" ftype="png" compare="sim_size"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2045 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="sim_size"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2046 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="sim_size"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2047 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="sim_size"/>
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2048 </output_collection>
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2049 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2050 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2051 <!-- test 30: pl.rank_genes_groups_dotplot -->
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2052 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2053 <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	2054 <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	2055 <param name="method" value="pl.rank_genes_groups_dotplot"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2056 <param name="gene_symbols" value="symbol"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2057 <param name="n_genes" value="10"/>
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2058 <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	2059 <param name="type" value="all"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2060 </conditional>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2061 <param name="log" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2062 <param name="use_raw" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2063 <param name="dendrogram" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2064 <param name="color_map" value="viridis"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2065 <section name="matplotlib_pyplot_scatter">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2066 <param name="linewidths" value="0" />
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2067 <param name="edgecolors" value="face"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2068 </section>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2069 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2070 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2071 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2072 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2073 <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	2074 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2075 <has_text_matching expression="sc.pl.rank_genes_groups_dotplot"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2076 <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	2077 <has_text_matching expression="log=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2078 <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	2079 <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	2080 <has_text_matching expression="color_map='viridis'"/>
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	2081 <has_text_matching expression="lw=0.0"/>
9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	2082 <has_text_matching expression="ec='face'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2083 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2084 </output>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2085 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2086 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2087 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2088 <!-- test 31: pl.rank_genes_groups_heatmap -->
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2089 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2090 <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	2091 <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	2092 <param name="method" value="pl.rank_genes_groups_heatmap"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2093 <param name="gene_symbols" value="symbol"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2094 <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	2095 <param name="log" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2096 <param name="use_raw" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2097 <param name="dendrogram" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2098 <param name="swap_axes" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2099 <param name="show_gene_labels" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2100 <section name="matplotlib_pyplot_imshow">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2101 <param name="cmap" value="viridis"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2102 <param name="interpolation" value="None"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2103 <param name="origin" value="upper"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2104 </section>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2105 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2106 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2107 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2108 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2109 <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	2110 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2111 <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	2112 <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	2113 <has_text_matching expression="log=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2114 <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	2115 <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	2116 <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	2117 <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	2118 <has_text_matching expression="cmap='viridis'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2119 <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	2120 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2121 </output>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2122 <output name="out_png" file="pl.rank_genes_groups_heatmap.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2123 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2124 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2125 <!-- test 32: pl.rank_genes_groups_matrixplot -->
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2126 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2127 <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	2128 <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	2129 <param name="method" value="pl.rank_genes_groups_matrixplot"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2130 <param name="gene_symbols" value="symbol"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2131 <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	2132 <param name="log" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2133 <param name="use_raw" value="False"/>
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="dendrogram" value="False"/>
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="swap_axes" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2136 <section name="matplotlib_pyplot_pcolor">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2137 <param name="cmap" value="viridis"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2138 <param name="edgecolors" value="face"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2139 <param name="snap" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2140 </section>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2141 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2142 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2143 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2144 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2145 <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	2146 <assert_contents>
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="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	2148 <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	2149 <has_text_matching expression="log=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2150 <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	2151 <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	2152 <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	2153 <has_text_matching expression="cmap='viridis'"/>
12 9b0cdb8cf6be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 6fc3a3aa54d7ece1fd8bfffe62ad7e2b620539e0 iuc parents: 11 diff changeset	2154 <has_text_matching expression="ec='face'"/>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2155 <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	2156 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2157 </output>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2158 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2159 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2160 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2161 <!-- test 33: 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	2162 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad" />
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2163 <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	2164 <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	2165 <param name="method" value="pl.rank_genes_groups_stacked_violin"/>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2166 <param name="gene_symbols" value="symbol"/>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2167 <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	2168 <param name="log" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2169 <param name="use_raw" value="False"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2170 <param name="dendrogram" value="True"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2171 <param name="swap_axes" value="True"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2172 <section name="violin_plot">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2173 <conditional name="stripplot">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2174 <param name="stripplot" value="True"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2175 <param name="jitter" value="True"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2176 <param name="size" value="1"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2177 </conditional>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2178 <param name="scale" value="width"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2179 </section>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2180 <param name="row_palette" value="muted"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2181 <param name="standard_scale" value="None"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2182 <section name="seaborn_violinplot">
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2183 <param name="bw" value="scott"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2184 <param name="linewidth" value="0"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2185 <param name="color" value="AliceBlue"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2186 <param name="palette" value="viridis"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2187 <param name="saturation" value="0.75"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2188 </section>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2189 </conditional>
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2190 <section name="advanced_common">
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2191 <param name="show_log" value="true" />
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2192 </section>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2193 <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	2194 <assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2195 <has_text_matching expression="sc.pl.rank_genes_groups_stacked_violin"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2196 <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	2197 <has_text_matching expression="log=False"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2198 <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	2199 <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	2200 <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	2201 <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	2202 <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	2203 <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	2204 <has_text_matching expression="scale='width'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2205 <has_text_matching expression="bw='scott'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2206 <has_text_matching expression="scale='width'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2207 <has_text_matching expression="linewidth=0.0"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2208 <has_text_matching expression="color='AliceBlue'"/>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2209 <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	2210 </assert_contents>
dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2211 </output>
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2212 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="sim_size"/>
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2213 </test>
11 95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2214 <test expect_num_outputs="2">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2215 <!-- test 34: pl.scatter log !-->
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2216 <param name="adata" value="pbmc68k_reduced.h5ad" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2217 <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	2218 <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	2219 <param name="method" value="pl.scatter"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2220 <conditional name="type">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2221 <param name="type" value="xy"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2222 <param name="x" value="n_genes"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2223 <param name="y" value="n_counts"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2224 <param name="log" value="True"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2225 <conditional name="layers">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2226 <param name="use_layers" value="false"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2227 </conditional>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2228 </conditional>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2229 <param name="use_raw" value="False"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2230 <param name="sort_order" value="True"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2231 <section name="plot">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2232 <param name="projection" value="2d"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2233 <param name="legend_loc" value="right margin"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2234 <param name="legend_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	2235 <param name="legend_fontweight" value="normal"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2236 <param name="palette" value="bwr"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2237 <param name="frameon" value="False"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2238 <param name="size" value="1"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2239 <param name="title" value="A title"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2240 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2241 </conditional>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2242 <section name="advanced_common">
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2243 <param name="show_log" value="true" />
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2244 </section>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2245 <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	2246 <assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2247 <has_text_matching expression="sc.pl.scatter"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2248 <has_text_matching expression="use_raw=False"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2249 <has_text_matching expression="sort_order=True"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2250 <has_text_matching expression="projection='2d'"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2251 <has_text_matching expression="legend_loc='right margin'"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2252 <has_text_matching expression="legend_fontsize=1"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2253 <has_text_matching expression="legend_fontweight='normal'"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2254 <has_text_matching expression="frameon=False"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2255 <has_text_matching expression="size=1.0"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2256 <has_text_matching expression="title='A title'"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2257 </assert_contents>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2258 </output>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2259 <output name="out_png" file="pl.scatter.pbmc68k_reduced.png" ftype="png" compare="sim_size"/>
95777145cb92 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d iuc parents: 10 diff changeset	2260 </test>
16 1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2261 <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	2262 <!-- test 35: pl.rank_genes_groups_dotplot with marker list -->
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2263 <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	2264 <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	2265 <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	2266 <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	2267 <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	2268 <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	2269 <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	2270 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2271 <param name="groupby" value="bulk_labels"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2272 <param name="log" value="False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2273 <param name="use_raw" value="False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2274 <param name="dendrogram" value="False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2275 <param name="color_map" value="viridis"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2276 <section name="matplotlib_pyplot_scatter">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2277 <param name="linewidths" value="0" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2278 <param name="edgecolors" value="face"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2279 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2280 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2281 <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	2282 <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	2283 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2284 <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	2285 <assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2286 <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	2287 <has_text_matching expression="groupby='bulk_labels'"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2288 <has_text_matching expression="log=False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2289 <has_text_matching expression="use_raw=False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2290 <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	2291 <has_text_matching expression="color_map='viridis'"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2292 <has_text_matching expression="lw=0.0"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2293 <has_text_matching expression="ec='face'"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2294 </assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2295 </output>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2296 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="sim_size"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2297 </test>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2298 <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	2299 <!-- test 36: pl.rank_genes_groups_dotplot with marker list -->
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2300 <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	2301 <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	2302 <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	2303 <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	2304 <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	2305 <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	2306 <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	2307 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2308 <param name="groupby" value="bulk_labels"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2309 <param name="log" value="False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2310 <param name="use_raw" value="False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2311 <param name="dendrogram" value="False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2312 <param name="color_map" value="viridis"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2313 <section name="matplotlib_pyplot_scatter">
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2314 <param name="linewidths" value="0" />
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2315 <param name="edgecolors" value="face"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2316 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2317 </conditional>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2318 <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	2319 <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	2320 </section>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2321 <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	2322 <assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2323 <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	2324 <has_text_matching expression="groupby='bulk_labels'"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2325 <has_text_matching expression="log=False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2326 <has_text_matching expression="use_raw=False"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2327 <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	2328 <has_text_matching expression="color_map='viridis'"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2329 <has_text_matching expression="lw=0.0"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2330 <has_text_matching expression="ec='face'"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2331 </assert_contents>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2332 </output>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2333 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_filtered_1.png" ftype="png" compare="sim_size"/>
1072ce66b426 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0ef475df22ba51263bb3d1db9f8797c723db35b0 iuc parents: 14 diff changeset	2334 </test>
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2335 </tests>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2336 <help><![CDATA[
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2337 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	2338 =========================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2339
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2340 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	2341 (`.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	2342
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2343 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	2344 <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	2345
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2346 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	2347 ========================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2348
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2349 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	2350 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	2351 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	2352 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	2353 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	2354
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2355 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	2356 <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	2357
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2358 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	2359 =================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2360
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2361 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	2362 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	2363 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	2364 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	2365 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	2366 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	2367 equal to zero.
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 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	2370 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	2371
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2372 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	2373 <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	2374
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2375 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	2376 ==================================
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 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	2379
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2380 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	2381 <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	2382
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2383 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	2384 ===================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2385
6 dbbe1ea8ecb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452" iuc parents: 5 diff changeset	2386 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	2387 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	2388
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2389 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	2390 <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	2391
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2392 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	2393 ============================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2394
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2395 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	2396
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2397 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	2398 category.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2399
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2400 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	2401 <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	2402
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2403 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	2404 ===========================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2405
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2406 Wraps `seaborn.clustermap
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2407 <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	2408 `anndata.AnnData`.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2409
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2410 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	2411 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	2412
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2413 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	2414 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	2415
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2416 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	2417
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2418 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	2419 <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	2420
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2421 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	2422 =========================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2423
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2424 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	2425 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	2426 plotted as boxplots.
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2427
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2428 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	2429
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2430 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	2431 <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	2432
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2433 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	2434 ===================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2435
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2436 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	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.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	2440
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2441 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	2442 ===============================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2443
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: 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.pca.html>`__
0 397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2446
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2447 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	2448 =====================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2449
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: 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.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	2452
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2453 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	2454 ======================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2455
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2456 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	2457 <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	2458
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2459 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	2460 =========================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2461
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2462 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	2463 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	2464
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2465 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	2466 <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	2467
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2468 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	2469 =================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2470
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2471 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	2472 <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	2473
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2474 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	2475 ==================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2476
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2477 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	2478 <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	2479
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2480 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	2481 ==============================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2482
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2483 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	2484 <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	2485
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2486 Branching trajectories and pseudotime, clustering: Plot groups and pseudotime (`pl.dpt_groups_pseudotime`)
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2487 ===========================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2488
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2489 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	2490 <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	2491
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2492 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	2493 =====================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2494
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2495 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	2496 <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	2497
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2498
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2499 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	2500 ====================================================================================================================================
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2501
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2502 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	2503
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2504 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	2505 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	2506 `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	2507
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2508 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	2509 <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	2510
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2511
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2512 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	2513 ==========================================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2514
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2515 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	2516 <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	2517
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2518 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	2519 ======================================================================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2520
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2521 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	2522 <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	2523
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2524 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	2525 ===============================================================================
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2526
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2527 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	2528 <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	2529
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2530 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	2531 ==================================================================================
1 e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2532
e4c0f5ee8e17 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5" iuc parents: 0 diff changeset	2533 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	2534 <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	2535
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2536 Marker genes: Plot ranking of genes as dotplot plot (`pl.rank_genes_groups_dotplot`)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2537 ====================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2538
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2539 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	2540 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_dotplot.html>`__
3 a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2541
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2542 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	2543 ====================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2544
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2545 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	2546 <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	2547
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2548 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	2549 ==========================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2550
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2551 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	2552 <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	2553
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2554 Marker genes: Plot ranking of genes as stacked violin plot (`pl.rank_genes_groups_stacked_violin`)
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2555 ==================================================================================================
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2556
a8f865950ac4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 3b41d687ff30583540d055f6995de00530cca81d" iuc parents: 2 diff changeset	2557 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	2558 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pl.rank_genes_groups_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	2559 ]]></help>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2560 <expand macro="citations"/>
397d2c97af05 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 92f85afaed0097d1879317a9f513093fce5481d6 iuc parents: diff changeset	2561 </tool>

Mercurial > repos > iuc > scanpy_plot

annotate plot.xml @ 16:1072ce66b426 draft