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comparison plot.xml @ 9:2644ebc71c2c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9a4fd56468fd032c995b9033267123e723fea927"
author iuc
date Mon, 12 Apr 2021 18:09:03 +0000
parents d2a2adbb0ef3
children c6b7bb9eb72f
comparison
equal deleted inserted replaced
8:d2a2adbb0ef3 9:2644ebc71c2c
1 <tool id="scanpy_plot" name="Plot" version="@galaxy_version@" profile="@profile@"> 1 <tool id="scanpy_plot" name="Plot" version="1.7.1+galaxy1" profile="@profile@">
2 <description> with scanpy</description> 2 <description> with scanpy</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
57 frameon=$method.plot.frameon) 57 frameon=$method.plot.frameon)
58 58
59 #else if $method.method == 'pl.heatmap' 59 #else if $method.method == 'pl.heatmap'
60 sc.pl.heatmap( 60 sc.pl.heatmap(
61 @CMD_param_plot_inputs@ 61 @CMD_param_plot_inputs@
62 #if str($method.gene_symbols) != ''
63 gene_symbols='$method.gene_symbols',
64 #end if
62 @CMD_params_inputs@ 65 @CMD_params_inputs@
63 @CMD_params_plots@ 66 @CMD_params_plots@
64 @CMD_pl_heatmap@) 67 @CMD_pl_heatmap@)
65 68
66 #else if $method.method == 'pl.dotplot' 69 #else if $method.method == 'pl.dotplot'
67 sc.pl.dotplot( 70 sc.pl.dotplot(
68 @CMD_param_plot_inputs@ 71 @CMD_param_plot_inputs@
72 #if str($method.gene_symbols) != ''
73 gene_symbols='$method.gene_symbols',
74 #end if
69 @CMD_params_inputs@ 75 @CMD_params_inputs@
70 @CMD_params_plots@ 76 @CMD_params_plots@
71 @CMD_pl_dotplot@) 77 @CMD_pl_dotplot@)
72 78
73 #else if $method.method == 'pl.violin' 79 #else if $method.method == 'pl.violin'
101 @CMD_params_seaborn_violinplot@) 107 @CMD_params_seaborn_violinplot@)
102 108
103 #else if $method.method == 'pl.stacked_violin' 109 #else if $method.method == 'pl.stacked_violin'
104 sc.pl.stacked_violin( 110 sc.pl.stacked_violin(
105 @CMD_param_plot_inputs@ 111 @CMD_param_plot_inputs@
112 #if str($method.gene_symbols) != ''
113 gene_symbols='$method.gene_symbols',
114 #end if
106 @CMD_params_inputs@ 115 @CMD_params_inputs@
107 @CMD_params_plots@ 116 @CMD_params_plots@
108 @CMD_pl_stacked_violin@) 117 @CMD_pl_stacked_violin@)
109 118
110 #else if $method.method == 'pl.matrixplot' 119 #else if $method.method == 'pl.matrixplot'
111 sc.pl.matrixplot( 120 sc.pl.matrixplot(
112 @CMD_param_plot_inputs@ 121 @CMD_param_plot_inputs@
122 #if str($method.gene_symbols) != ''
123 gene_symbols='$method.gene_symbols',
124 #end if
113 @CMD_params_inputs@ 125 @CMD_params_inputs@
114 @CMD_params_plots@ 126 @CMD_params_plots@
115 @CMD_pl_matrixplot@) 127 @CMD_pl_matrixplot@)
116 128
117 #else if $method.method == 'pl.clustermap' 129 #else if $method.method == 'pl.clustermap'
472 <expand macro="param_title"/> 484 <expand macro="param_title"/>
473 </section> 485 </section>
474 </when> 486 </when>
475 <when value="pl.heatmap"> 487 <when value="pl.heatmap">
476 <expand macro="params_inputs"/> 488 <expand macro="params_inputs"/>
489 <expand macro="gene_symbols"/>
477 <expand macro="params_plots"/> 490 <expand macro="params_plots"/>
478 <expand macro="pl_heatmap"/> 491 <expand macro="pl_heatmap"/>
479 </when> 492 </when>
480 <when value="pl.dotplot"> 493 <when value="pl.dotplot">
481 <expand macro="params_inputs"/> 494 <expand macro="params_inputs"/>
495 <expand macro="gene_symbols"/>
482 <expand macro="params_plots"/> 496 <expand macro="params_plots"/>
483 <expand macro="pl_dotplot"/> 497 <expand macro="pl_dotplot"/>
484 </when> 498 </when>
485 <when value="pl.violin"> 499 <when value="pl.violin">
486 <conditional name="key_variables"> 500 <conditional name="key_variables">
521 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/> 535 <param argument="rotation" type="float" value="" optional="true" label="Rotation of xtick labels" help=""/>
522 <expand macro="seaborn_violinplot"/> 536 <expand macro="seaborn_violinplot"/>
523 </when> 537 </when>
524 <when value="pl.stacked_violin"> 538 <when value="pl.stacked_violin">
525 <expand macro="params_inputs"/> 539 <expand macro="params_inputs"/>
540 <expand macro="gene_symbols"/>
526 <expand macro="params_plots"/> 541 <expand macro="params_plots"/>
527 <expand macro="pl_stacked_violin"/> 542 <expand macro="pl_stacked_violin"/>
528 </when> 543 </when>
529 <when value="pl.matrixplot"> 544 <when value="pl.matrixplot">
530 <expand macro="params_inputs"/> 545 <expand macro="params_inputs"/>
546 <expand macro="gene_symbols"/>
531 <expand macro="params_plots"/> 547 <expand macro="params_plots"/>
532 <expand macro="pl_matrixplot"/> 548 <expand macro="pl_matrixplot"/>
533 </when> 549 </when>
534 <when value="pl.clustermap"> 550 <when value="pl.clustermap">
535 <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."> 551 <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.">
915 </assert_contents> 931 </assert_contents>
916 </output> 932 </output>
917 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/> 933 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="sim_size"/>
918 </test> 934 </test>
919 <test> 935 <test>
936 <!-- test 2.1: pl.heatmap with symbols !-->
937 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
938 <param name="format" value="png"/>
939 <conditional name="method">
940 <param name="method" value="pl.heatmap"/>
941 <conditional name="var_names">
942 <param name="type" value="custom"/>
943 <param name="var_names" value="Fog1,EKLF,SCL"/>
944 </conditional>
945 <param name="groupby" value="cell_type"/>
946 <param name="gene_symbols" value="symbol"/>
947 <param name="num_categories" value="7"/>
948 <param name="log" value="False"/>
949 <param name="use_raw" value="False"/>
950 <conditional name="figsize">
951 <param name="test" value="yes"/>
952 <param name="width" value="10" />
953 <param name="height" value="3"/>
954 </conditional>
955 <param name="dendrogram" value="True"/>
956 <param name="swap_axes" value="True"/>
957 <param name="show_gene_labels" value="True"/>
958 <section name="matplotlib_pyplot_imshow">
959 <param name="cmap" value="YlGnBu"/>
960 <param name="interpolation" value="None"/>
961 <param name="origin" value="upper"/>
962 </section>
963 </conditional>
964 <section name="advanced_common">
965 <param name="show_log" value="true" />
966 </section>
967 <output name="hidden_output">
968 <assert_contents>
969 <has_text_matching expression="sc.pl.heatmap"/>
970 <has_text_matching expression="gene_symbols='symbol'"/>
971 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
972 <has_text_matching expression="groupby='cell_type'"/>
973 <has_text_matching expression="log=False"/>
974 <has_text_matching expression="use_raw=False"/>
975 <has_text_matching expression="num_categories=7"/>
976 <has_text_matching expression="dendrogram=True"/>
977 <has_text_matching expression="figsize=\(10, 3\)"/>
978 <has_text_matching expression="swap_axes=True"/>
979 <has_text_matching expression="show_gene_labels=True"/>
980 <has_text_matching expression="cmap='YlGnBu'"/>
981 <has_text_matching expression="origin='upper'"/>
982 </assert_contents>
983 </output>
984 </test>
985 <test>
920 <!-- test 3: pl.dotplot !--> 986 <!-- test 3: pl.dotplot !-->
921 <param name="adata" value="pbmc68k_reduced.h5ad" /> 987 <param name="adata" value="pbmc68k_reduced.h5ad" />
922 <param name="format" value="png"/> 988 <param name="format" value="png"/>
923 <conditional name="method"> 989 <conditional name="method">
924 <param name="method" value="pl.dotplot"/> 990 <param name="method" value="pl.dotplot"/>
974 </assert_contents> 1040 </assert_contents>
975 </output> 1041 </output>
976 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/> 1042 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="sim_size"/>
977 </test> 1043 </test>
978 <test> 1044 <test>
1045 <!-- test 3.1: pl.dotplot with symbols !-->
1046 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
1047 <param name="format" value="png"/>
1048 <conditional name="method">
1049 <param name="method" value="pl.dotplot"/>
1050 <conditional name="var_names">
1051 <param name="type" value="custom"/>
1052 <param name="var_names" value="Fog1,EKLF,SCL"/>
1053 </conditional>
1054 <param name="groupby" value="cell_type"/>
1055 <param name="gene_symbols" value="symbol"/>
1056 <param name="num_categories" value="7"/>
1057 <param name="log" value="False"/>
1058 <param name="use_raw" value="False"/>
1059 <param name="dendrogram" value="True"/>
1060 <section name="matplotlib_pyplot_imshow">
1061 <param name="cmap" value="YlGnBu"/>
1062 <param name="interpolation" value="None"/>
1063 <param name="origin" value="upper"/>
1064 </section>
1065 </conditional>
1066 <section name="advanced_common">
1067 <param name="show_log" value="true" />
1068 </section>
1069 <output name="hidden_output">
1070 <assert_contents>
1071 <has_text_matching expression="sc.pl.dotplot"/>
1072 <has_text_matching expression="gene_symbols='symbol'"/>
1073 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
1074 <has_text_matching expression="groupby='cell_type'"/>
1075 <has_text_matching expression="log=False"/>
1076 <has_text_matching expression="use_raw=False"/>
1077 <has_text_matching expression="num_categories=7"/>
1078 <has_text_matching expression="dendrogram=True"/>
1079 </assert_contents>
1080 </output>
1081 </test>
1082 <test>
979 <!-- test 4: pl.violin !--> 1083 <!-- test 4: pl.violin !-->
980 <param name="adata" value="pbmc68k_reduced.h5ad" /> 1084 <param name="adata" value="pbmc68k_reduced.h5ad" />
981 <param name="format" value="png"/> 1085 <param name="format" value="png"/>
982 <conditional name="method"> 1086 <conditional name="method">
983 <param name="method" value="pl.violin"/> 1087 <param name="method" value="pl.violin"/>
1091 </assert_contents> 1195 </assert_contents>
1092 </output> 1196 </output>
1093 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/> 1197 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="sim_size"/>
1094 </test> 1198 </test>
1095 <test> 1199 <test>
1200 <!-- test 5.1: pl.stacked_violin with symbols !-->
1201 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
1202 <param name="format" value="png"/>
1203 <conditional name="method">
1204 <param name="method" value="pl.stacked_violin"/>
1205 <conditional name="var_names">
1206 <param name="type" value="custom"/>
1207 <param name="var_names" value="Fog1,EKLF,SCL"/>
1208 </conditional>
1209 <param name="groupby" value="cell_type"/>
1210 <param name="gene_symbols" value="symbol"/>
1211 <param name="num_categories" value="7"/>
1212 <param name="log" value="False"/>
1213 <param name="use_raw" value="False"/>
1214 <param name="dendrogram" value="True"/>
1215 <param name="swap_axes" value="True"/>
1216 </conditional>
1217 <section name="advanced_common">
1218 <param name="show_log" value="true" />
1219 </section>
1220 <output name="hidden_output">
1221 <assert_contents>
1222 <has_text_matching expression="sc.pl.stacked_violin"/>
1223 <has_text_matching expression="gene_symbols='symbol'"/>
1224 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
1225 <has_text_matching expression="groupby='cell_type'"/>
1226 <has_text_matching expression="log=False"/>
1227 <has_text_matching expression="use_raw=False"/>
1228 <has_text_matching expression="num_categories=7"/>
1229 <has_text_matching expression="dendrogram=True"/>
1230 <has_text_matching expression="swap_axes=True"/>
1231 </assert_contents>
1232 </output>
1233 </test>
1234 <test>
1096 <!-- test 6: pl.matrixplot !--> 1235 <!-- test 6: pl.matrixplot !-->
1097 <param name="adata" value="krumsiek11.h5ad" /> 1236 <param name="adata" value="krumsiek11.h5ad" />
1098 <param name="format" value="png"/> 1237 <param name="format" value="png"/>
1099 <conditional name="method"> 1238 <conditional name="method">
1100 <param name="method" value="pl.matrixplot"/> 1239 <param name="method" value="pl.matrixplot"/>
1133 <has_text_matching expression="edgecolors='face'"/> 1272 <has_text_matching expression="edgecolors='face'"/>
1134 <has_text_matching expression="snap=False"/> 1273 <has_text_matching expression="snap=False"/>
1135 </assert_contents> 1274 </assert_contents>
1136 </output> 1275 </output>
1137 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/> 1276 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="sim_size"/>
1277 </test>
1278 <test>
1279 <!-- test 6.1: pl.matrixplot with symbols !-->
1280 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad" />
1281 <param name="format" value="png"/>
1282 <conditional name="method">
1283 <param name="method" value="pl.matrixplot"/>
1284 <conditional name="var_names">
1285 <param name="type" value="custom"/>
1286 <param name="var_names" value="Fog1,EKLF,SCL"/>
1287 </conditional>
1288 <param name="groupby" value="cell_type"/>
1289 <param name="gene_symbols" value="symbol"/>
1290 <param name="num_categories" value="7"/>
1291 <param name="log" value="False"/>
1292 <param name="use_raw" value="False"/>
1293 <conditional name="figsize">
1294 <param name="test" value="yes"/>
1295 <param name="width" value="10" />
1296 <param name="height" value="3"/>
1297 </conditional>
1298 <param name="dendrogram" value="True"/>
1299 <param name="swap_axes" value="False"/>
1300 </conditional>
1301 <section name="advanced_common">
1302 <param name="show_log" value="true" />
1303 </section>
1304 <output name="hidden_output">
1305 <assert_contents>
1306 <has_text_matching expression="sc.pl.matrixplot"/>
1307 <has_text_matching expression="gene_symbols='symbol'"/>
1308 <has_text_matching expression="var_names=\['Fog1', 'EKLF', 'SCL'\]" />
1309 <has_text_matching expression="groupby='cell_type'"/>
1310 <has_text_matching expression="log=False"/>
1311 <has_text_matching expression="use_raw=False"/>
1312 <has_text_matching expression="num_categories=7"/>
1313 <has_text_matching expression="dendrogram=True"/>
1314 <has_text_matching expression="swap_axes=False"/>
1315 </assert_contents>
1316 </output>
1138 </test> 1317 </test>
1139 <test> 1318 <test>
1140 <!-- test 7: pl.clustermap !--> 1319 <!-- test 7: pl.clustermap !-->
1141 <param name="adata" value="krumsiek11.h5ad" /> 1320 <param name="adata" value="krumsiek11.h5ad" />
1142 <param name="format" value="png"/> 1321 <param name="format" value="png"/>