Mercurial > repos > iuc > scanpy_plot

comparison plot.xml @ 16:ff6da5117343 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
author iuc
date Thu, 03 Oct 2024 22:41:00 +0000
parents aa8abbf399b3
children 413ffec60330
comparison
equal deleted inserted replaced
15:8b2c8dcd9519 16:ff6da5117343
73 #end if 73 #end if
74 @CMD_PARAM_LEGEND_FONTSIZE@ 74 @CMD_PARAM_LEGEND_FONTSIZE@
75 legend_fontweight='$method.plot.legend_fontweight', 75 legend_fontweight='$method.plot.legend_fontweight',
76 #if $method.plot.color_map: 76 #if $method.plot.color_map:
77 color_map='$method.plot.color_map', 77 color_map='$method.plot.color_map',
78 #end if 78 #end if
79 #if $method.plot.palette: 79 #if $method.plot.palette:
80 palette=['$method.plot.palette'], 80 palette=['$method.plot.palette'],
81 #end if 81 #end if
82 frameon=$method.plot.frameon, 82 frameon=$method.plot.frameon,
83 @CMD_PARAM_SIZE@ 83 @CMD_PARAM_SIZE@
96 96
97 #else if str($method.method) == 'pl.dotplot': 97 #else if str($method.method) == 'pl.dotplot':
98 @CMD_VAR_NAMES_HEADER_CHECK@ 98 @CMD_VAR_NAMES_HEADER_CHECK@
99 sc.pl.dotplot( 99 sc.pl.dotplot(
100 @CMD_PARAM_PLOT_INPUTS@ 100 @CMD_PARAM_PLOT_INPUTS@
101 @CMD_PARAMS_INPUTS@ 101 @CMD_PARAMS_INPUTS@
102 @CMD_PARAM_GENE_SYMBOLS@ 102 @CMD_PARAM_GENE_SYMBOLS@
103 @CMD_PARAMS_PLOTS@ 103 @CMD_PARAMS_PLOTS@
104 @CMD_PL_DOTPLOT@ 104 @CMD_PL_DOTPLOT@
105 @CMD_SHOW_NONE@) 105 @CMD_SHOW_NONE@)
106 106
257 use_raw=$method.use_raw, 257 use_raw=$method.use_raw,
258 sort_order=$method.sort_order, 258 sort_order=$method.sort_order,
259 @CMD_PARAM_GROUPS@ 259 @CMD_PARAM_GROUPS@
260 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@ 260 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
261 @CMD_SCATTER_OUTINE@ 261 @CMD_SCATTER_OUTINE@
262 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@ 262 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
263 @CMD_SHOW_NONE@) 263 @CMD_SHOW_NONE@)
264 264
265 #else if str($method.method) == 'pl.tsne': 265 #else if str($method.method) == 'pl.tsne':
266 sc.pl.tsne( 266 sc.pl.tsne(
267 @CMD_PARAM_PLOT_INPUTS@ 267 @CMD_PARAM_PLOT_INPUTS@
272 arrows=$method.arrows, 272 arrows=$method.arrows,
273 sort_order=$method.sort_order, 273 sort_order=$method.sort_order,
274 @CMD_PARAM_GROUPS@ 274 @CMD_PARAM_GROUPS@
275 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@ 275 @CMD_PARAMS_PL_ATTRIBUTE_SECTION@
276 @CMD_SCATTER_OUTINE@ 276 @CMD_SCATTER_OUTINE@
277 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@ 277 @CMD_SECTION_MATPLOTLIB_PYPLOT_SCATTER@
278 @CMD_PARAM_LAYER@ 278 @CMD_PARAM_LAYER@
279 @CMD_SHOW_NONE@) 279 @CMD_SHOW_NONE@)
280 280
281 #else if str($method.method) == 'pl.umap': 281 #else if str($method.method) == 'pl.umap':
282 sc.pl.umap( 282 sc.pl.umap(
364 sc.pl.paga( 364 sc.pl.paga(
365 @CMD_PARAM_PLOT_INPUTS@ 365 @CMD_PARAM_PLOT_INPUTS@
366 @CMD_PARAMS_PL_PAGA@ 366 @CMD_PARAMS_PL_PAGA@
367 @CMD_SHOW_NONE@) 367 @CMD_SHOW_NONE@)
368 368
369 @CMD_ANNDATA_WRITE_OUTPUTS@
370
369 #else if str($method.method) == 'pl.paga_compare': 371 #else if str($method.method) == 'pl.paga_compare':
370 sc.pl.paga_compare( 372 sc.pl.paga_compare(
371 @CMD_PARAM_PLOT_INPUTS@ 373 @CMD_PARAM_PLOT_INPUTS@
372 @CMD_PARAMS_PL_PAGA@ 374 @CMD_PARAMS_PL_PAGA@
373 @CMD_PARAM_PL_COMPONENTS@ 375 @CMD_PARAM_PL_COMPONENTS@
377 #end if 379 #end if
378 @CMD_PARAM_LEGEND_FONTSIZE@ 380 @CMD_PARAM_LEGEND_FONTSIZE@
379 legend_fontweight='$method.plot.legend_fontweight', 381 legend_fontweight='$method.plot.legend_fontweight',
380 #if $method.plot.color_map: 382 #if $method.plot.color_map:
381 color_map='$method.plot.color_map', 383 color_map='$method.plot.color_map',
382 #end if 384 #end if
383 #if $method.plot.palette: 385 #if $method.plot.palette:
384 palette=['$method.plot.palette'], 386 palette=['$method.plot.palette'],
385 #end if 387 #end if
386 @CMD_PARAM_SIZE@ 388 @CMD_PARAM_SIZE@
387 @CMD_PARAM_TITLE@ 389 @CMD_PARAM_TITLE@
641 <expand macro="param_use_raw" falsevalue="None"/> 643 <expand macro="param_use_raw" falsevalue="None"/>
642 <section name="violin_plot" title="Violin plot attributes"> 644 <section name="violin_plot" title="Violin plot attributes">
643 <expand macro="conditional_stripplot"/> 645 <expand macro="conditional_stripplot"/>
644 <conditional name="multi_panel"> 646 <conditional name="multi_panel">
645 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when 'groupby is not provided"> 647 <param argument="multi_panel" type="select" label="Display keys in multiple panels" help="Also when 'groupby is not provided">
646 <option value="None" selected="true">No</option> 648 <option value="None" selected="true">No</option>
647 <option value="True">Yes</option> 649 <option value="True">Yes</option>
648 </param> 650 </param>
649 <when value="None"/> 651 <when value="None"/>
650 <when value="True"> 652 <when value="True">
651 <!-- <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure"/> 653 <!-- <param argument="width" type="integer" min="0" value="" optional="true" label="Width of the figure"/>
992 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter> 994 <filter>format == 'svg' and method['method'] == 'pl.rank_genes_groups_violin'</filter>
993 </collection> 995 </collection>
994 <data name="hidden_output" format="txt" label="Log file" hidden="true" > 996 <data name="hidden_output" format="txt" label="Log file" hidden="true" >
995 <filter>advanced_common['show_log']</filter> 997 <filter>advanced_common['show_log']</filter>
996 </data> 998 </data>
999 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix">
1000 <filter>method['method'] == 'pl.paga'</filter>
1001 </data>
997 </outputs> 1002 </outputs>
998 <tests> 1003 <tests>
999 <!-- test 1 --> 1004 <!-- test 1 -->
1000 <test expect_num_outputs="2"> 1005 <test expect_num_outputs="2">
1001 <param name="adata" value="pbmc68k_reduced.h5ad"/> 1006 <param name="adata" value="pbmc68k_reduced.h5ad"/>
1034 <has_text_matching expression="size=1.0"/> 1039 <has_text_matching expression="size=1.0"/>
1035 </assert_contents> 1040 </assert_contents>
1036 </output> 1041 </output>
1037 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="image_diff"/> 1042 <output name="out_png" file="pl.scatter.umap.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
1038 </test> 1043 </test>
1039 1044
1040 <!-- test 2 --> 1045 <!-- test 2 -->
1041 <test expect_num_outputs="2"> 1046 <test expect_num_outputs="2">
1042 <param name="adata" value="krumsiek11.h5ad"/> 1047 <param name="adata" value="krumsiek11.h5ad"/>
1043 <param name="format" value="png"/> 1048 <param name="format" value="png"/>
1044 <conditional name="method"> 1049 <conditional name="method">
1074 <has_text_matching expression="title='A title'"/> 1079 <has_text_matching expression="title='A title'"/>
1075 </assert_contents> 1080 </assert_contents>
1076 </output> 1081 </output>
1077 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="image_diff"/> 1082 <output name="out_png" file="pl.scatter.krumsiek11.png" ftype="png" compare="image_diff"/>
1078 </test> 1083 </test>
1079 1084
1080 <!-- test 3 --> 1085 <!-- test 3 -->
1081 <test expect_num_outputs="2"> 1086 <test expect_num_outputs="2">
1082 <param name="adata" value="pbmc68k_reduced.h5ad"/> 1087 <param name="adata" value="pbmc68k_reduced.h5ad"/>
1083 <param name="format" value="png"/> 1088 <param name="format" value="png"/>
1084 <conditional name="method"> 1089 <conditional name="method">
1152 <has_text_matching expression="origin='upper'"/> 1157 <has_text_matching expression="origin='upper'"/>
1153 </assert_contents> 1158 </assert_contents>
1154 </output> 1159 </output>
1155 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="image_diff"/> 1160 <output name="out_png" file="pl.heatmap.krumsiek11.png" ftype="png" compare="image_diff"/>
1156 </test> 1161 </test>
1157 1162
1158 <!-- test 5 --> 1163 <!-- test 5 -->
1159 <test expect_num_outputs="2"> 1164 <test expect_num_outputs="2">
1160 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/> 1165 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
1161 <param name="format" value="png"/> 1166 <param name="format" value="png"/>
1162 <conditional name="method"> 1167 <conditional name="method">
1198 <has_text_matching expression="cmap='YlGnBu'"/> 1203 <has_text_matching expression="cmap='YlGnBu'"/>
1199 <has_text_matching expression="origin='upper'"/> 1204 <has_text_matching expression="origin='upper'"/>
1200 </assert_contents> 1205 </assert_contents>
1201 </output> 1206 </output>
1202 </test> 1207 </test>
1203 1208
1204 <!-- test 6 --> 1209 <!-- test 6 -->
1205 <test expect_num_outputs="2"> 1210 <test expect_num_outputs="2">
1206 <param name="adata" value="pbmc68k_reduced.h5ad"/> 1211 <param name="adata" value="pbmc68k_reduced.h5ad"/>
1207 <param name="format" value="png"/> 1212 <param name="format" value="png"/>
1208 <conditional name="method"> 1213 <conditional name="method">
1248 <has_text_matching expression="dot_min=0.1"/> 1253 <has_text_matching expression="dot_min=0.1"/>
1249 </assert_contents> 1254 </assert_contents>
1250 </output> 1255 </output>
1251 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="image_diff"/> 1256 <output name="out_png" file="pl.dotplot.krumsiek11.png" ftype="png" compare="image_diff"/>
1252 </test> 1257 </test>
1253 1258
1254 <!-- test 7 --> 1259 <!-- test 7 -->
1255 <test expect_num_outputs="2"> 1260 <test expect_num_outputs="2">
1256 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/> 1261 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
1257 <param name="format" value="png"/> 1262 <param name="format" value="png"/>
1258 <conditional name="method"> 1263 <conditional name="method">
1260 <conditional name="var_names"> 1265 <conditional name="var_names">
1261 <param name="type" value="custom"/> 1266 <param name="type" value="custom"/>
1262 <param name="var_names" value="Fog1,EKLF,SCL"/> 1267 <param name="var_names" value="Fog1,EKLF,SCL"/>
1263 </conditional> 1268 </conditional>
1264 <param name="gene_symbols" value="symbol"/> 1269 <param name="gene_symbols" value="symbol"/>
1265 <param name="groupby" value="cell_type"/> 1270 <param name="groupby" value="cell_type"/>
1266 <param name="dendrogram" value="True"/> 1271 <param name="dendrogram" value="True"/>
1267 <section name="matplotlib_pyplot_imshow"> 1272 <section name="matplotlib_pyplot_imshow">
1268 <param name="cmap" value="YlGnBu"/> 1273 <param name="cmap" value="YlGnBu"/>
1269 </section> 1274 </section>
1270 </conditional> 1275 </conditional>
1282 <has_text_matching expression="num_categories=7"/> 1287 <has_text_matching expression="num_categories=7"/>
1283 <has_text_matching expression="dendrogram=True"/> 1288 <has_text_matching expression="dendrogram=True"/>
1284 </assert_contents> 1289 </assert_contents>
1285 </output> 1290 </output>
1286 </test> 1291 </test>
1287 1292
1288 <!-- test 8 --> 1293 <!-- test 8 -->
1289 <test expect_num_outputs="2"> 1294 <test expect_num_outputs="2">
1290 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/> 1295 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
1291 <param name="format" value="png"/> 1296 <param name="format" value="png"/>
1292 <conditional name="method"> 1297 <conditional name="method">
1293 <param name="method" value="pl.tracksplot"/> 1298 <param name="method" value="pl.tracksplot"/>
1294 <param name="gene_symbols" value="symbol"/> 1299 <param name="gene_symbols" value="symbol"/>
1295 <param name="groupby" value="cell_type"/> 1300 <param name="groupby" value="cell_type"/>
1296 <param name="dendrogram" value="True"/> 1301 <param name="dendrogram" value="True"/>
1297 <section name="matplotlib_pyplot_imshow"> 1302 <section name="matplotlib_pyplot_imshow">
1298 <param name="cmap" value="YlGnBu"/> 1303 <param name="cmap" value="YlGnBu"/>
1299 </section> 1304 </section>
1300 </conditional> 1305 </conditional>
1321 <conditional name="method"> 1326 <conditional name="method">
1322 <param name="method" value="pl.violin"/> 1327 <param name="method" value="pl.violin"/>
1323 <conditional name="key_variables"> 1328 <conditional name="key_variables">
1324 <param name="type" value="custom"/> 1329 <param name="type" value="custom"/>
1325 <param name="keys" value="n_genes, percent_mito, n_counts"/> 1330 <param name="keys" value="n_genes, percent_mito, n_counts"/>
1326 </conditional> 1331 </conditional>
1327 <section name="violin_plot"> 1332 <section name="violin_plot">
1328 <conditional name="multi_panel"> 1333 <conditional name="multi_panel">
1329 <param name="multi_panel" value="True"/> 1334 <param name="multi_panel" value="True"/>
1330 </conditional> 1335 </conditional>
1331 </section> 1336 </section>
1350 <has_text_matching expression="saturation=0.75"/> 1355 <has_text_matching expression="saturation=0.75"/>
1351 </assert_contents> 1356 </assert_contents>
1352 </output> 1357 </output>
1353 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="image_diff" eps="0.4"/> 1358 <output name="out_png" file="pl.violin.pbmc68k_reduced_custom.png" ftype="png" compare="image_diff" eps="0.4"/>
1354 </test> 1359 </test>
1355 1360
1356 <!-- test 10 --> 1361 <!-- test 10 -->
1357 <test expect_num_outputs="2"> 1362 <test expect_num_outputs="2">
1358 <param name="adata" value="krumsiek11.h5ad"/> 1363 <param name="adata" value="krumsiek11.h5ad"/>
1359 <param name="format" value="png"/> 1364 <param name="format" value="png"/>
1360 <conditional name="method"> 1365 <conditional name="method">
1389 <has_text_matching expression="saturation=0.75"/> 1394 <has_text_matching expression="saturation=0.75"/>
1390 </assert_contents> 1395 </assert_contents>
1391 </output> 1396 </output>
1392 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="image_diff" eps="1.1"/> 1397 <output name="out_png" file="pl.stacked_violin.krumsiek11.png" ftype="png" compare="image_diff" eps="1.1"/>
1393 </test> 1398 </test>
1394 1399
1395 <!-- test 11 --> 1400 <!-- test 11 -->
1396 <test expect_num_outputs="2"> 1401 <test expect_num_outputs="2">
1397 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/> 1402 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
1398 <param name="format" value="png"/> 1403 <param name="format" value="png"/>
1399 <conditional name="method"> 1404 <conditional name="method">
1423 <has_text_matching expression="swap_axes=True"/> 1428 <has_text_matching expression="swap_axes=True"/>
1424 </assert_contents> 1429 </assert_contents>
1425 </output> 1430 </output>
1426 <output name="out_png" file="pl.stacked_violin_pp.filter_genes_dispersion.krumsiek11-seurat.png" compare="image_diff" eps="0.6"/> 1431 <output name="out_png" file="pl.stacked_violin_pp.filter_genes_dispersion.krumsiek11-seurat.png" compare="image_diff" eps="0.6"/>
1427 </test> 1432 </test>
1428 1433
1429 <!-- test 12 --> 1434 <!-- test 12 -->
1430 <test expect_num_outputs="2"> 1435 <test expect_num_outputs="2">
1431 <param name="adata" value="krumsiek11.h5ad"/> 1436 <param name="adata" value="krumsiek11.h5ad"/>
1432 <param name="format" value="png"/> 1437 <param name="format" value="png"/>
1433 <conditional name="method"> 1438 <conditional name="method">
1452 <has_text_matching expression="snap=False"/> 1457 <has_text_matching expression="snap=False"/>
1453 </assert_contents> 1458 </assert_contents>
1454 </output> 1459 </output>
1455 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="image_diff"/> 1460 <output name="out_png" file="pl.matrixplot.krumsiek11.png" ftype="png" compare="image_diff"/>
1456 </test> 1461 </test>
1457 1462
1458 <!-- test 13 --> 1463 <!-- test 13 -->
1459 <test expect_num_outputs="2"> 1464 <test expect_num_outputs="2">
1460 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/> 1465 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
1461 <param name="format" value="png"/> 1466 <param name="format" value="png"/>
1462 <conditional name="method"> 1467 <conditional name="method">
1489 <has_text_matching expression="dendrogram=True"/> 1494 <has_text_matching expression="dendrogram=True"/>
1490 <has_text_matching expression="swap_axes=False"/> 1495 <has_text_matching expression="swap_axes=False"/>
1491 </assert_contents> 1496 </assert_contents>
1492 </output> 1497 </output>
1493 </test> 1498 </test>
1494 1499
1495 <!-- test 14 --> 1500 <!-- test 14 -->
1496 <test expect_num_outputs="2"> 1501 <test expect_num_outputs="2">
1497 <param name="adata" value="krumsiek11.h5ad"/> 1502 <param name="adata" value="krumsiek11.h5ad"/>
1498 <param name="format" value="png"/> 1503 <param name="format" value="png"/>
1499 <conditional name="method"> 1504 <conditional name="method">
1518 <has_text_matching expression="row_cluster=False"/> 1523 <has_text_matching expression="row_cluster=False"/>
1519 </assert_contents> 1524 </assert_contents>
1520 </output> 1525 </output>
1521 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="image_diff"/> 1526 <output name="out_png" file="pl.clustermap.krumsiek11.png" ftype="png" compare="image_diff"/>
1522 </test> 1527 </test>
1523 1528
1524 <!-- test 15 --> 1529 <!-- test 15 -->
1525 <test expect_num_outputs="2"> 1530 <test expect_num_outputs="2">
1526 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/> 1531 <param name="adata" value="pp.filter_genes_dispersion.krumsiek11-seurat.h5ad"/>
1527 <param name="format" value="png"/> 1532 <param name="format" value="png"/>
1528 <conditional name="method"> 1533 <conditional name="method">
1545 <has_text_matching expression="saturation=0.5"/> 1550 <has_text_matching expression="saturation=0.5"/>
1546 </assert_contents> 1551 </assert_contents>
1547 </output> 1552 </output>
1548 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="image_diff"/> 1553 <output name="out_png" file="pl.highest_expr_genes.filter_genes_dispersion.krumsiek11-seurat.png" ftype="png" compare="image_diff"/>
1549 </test> 1554 </test>
1550 1555
1551 <!-- test 16 --> 1556 <!-- test 16 -->
1552 <test expect_num_outputs="2"> 1557 <test expect_num_outputs="2">
1553 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad"/> 1558 <param name="adata" value="pp.highly_variable_genes.seurat.blobs.h5ad"/>
1554 <param name="format" value="png"/> 1559 <param name="format" value="png"/>
1555 <conditional name="method"> 1560 <conditional name="method">
1556 <param name="method" value="pl.highly_variable_genes"/> 1561 <param name="method" value="pl.highly_variable_genes"/>
1557 </conditional> 1562 </conditional>
1558 <section name="advanced_common"> 1563 <section name="advanced_common">
1559 <param name="show_log" value="true"/> 1564 <param name="show_log" value="true"/>
1560 </section> 1565 </section>
1561 <output name="hidden_output"> 1566 <output name="hidden_output">
1566 <has_text_matching expression="highly_variable_genes=True"/> 1571 <has_text_matching expression="highly_variable_genes=True"/>
1567 </assert_contents> 1572 </assert_contents>
1568 </output> 1573 </output>
1569 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="image_diff"/> 1574 <output name="out_png" file="pl.highly_variable_genes.seurat.blobs.png" ftype="png" compare="image_diff"/>
1570 </test> 1575 </test>
1571 1576
1572 <!-- test 17 --> 1577 <!-- test 17 -->
1573 <test expect_num_outputs="2"> 1578 <test expect_num_outputs="2">
1574 <param name="adata" value="pp.scrublet.krumsiek11.h5ad"/> 1579 <param name="adata" value="pp.scrublet.krumsiek11.h5ad"/>
1575 <param name="format" value="png"/> 1580 <param name="format" value="png"/>
1576 <conditional name="method"> 1581 <conditional name="method">
1577 <param name="method" value="pl.scrublet_score_distribution"/> 1582 <param name="method" value="pl.scrublet_score_distribution"/>
1578 </conditional> 1583 </conditional>
1579 <section name="advanced_common"> 1584 <section name="advanced_common">
1580 <param name="show_log" value="true"/> 1585 <param name="show_log" value="true"/>
1581 </section> 1586 </section>
1582 <output name="hidden_output"> 1587 <output name="hidden_output">
1634 <has_text_matching expression="hspace=0.25"/> 1639 <has_text_matching expression="hspace=0.25"/>
1635 </assert_contents> 1640 </assert_contents>
1636 </output> 1641 </output>
1637 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/> 1642 <output name="out_pdf" file="pl.pca.pbmc68k_reduced.CD3D_CD79A_components_2d.pdf" ftype="pdf" compare="sim_size"/>
1638 </test> 1643 </test>
1639 1644
1640 <!-- test 19 --> 1645 <!-- test 19 -->
1641 <test expect_num_outputs="2"> 1646 <test expect_num_outputs="2">
1642 <param name="adata" value="pp.pca.krumsiek11.h5ad"/> 1647 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
1643 <param name="format" value="png"/> 1648 <param name="format" value="png"/>
1644 <conditional name="method"> 1649 <conditional name="method">
1654 <has_text_matching expression="components=\[1, 2, 3\]"/> 1659 <has_text_matching expression="components=\[1, 2, 3\]"/>
1655 </assert_contents> 1660 </assert_contents>
1656 </output> 1661 </output>
1657 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="image_diff"/> 1662 <output name="out_png" file="pl.pca_loadings.pp.pca.krumsiek11.png" compare="image_diff"/>
1658 </test> 1663 </test>
1659 1664
1660 <!-- test 20 --> 1665 <!-- test 20 -->
1661 <test expect_num_outputs="2"> 1666 <test expect_num_outputs="2">
1662 <param name="adata" value="pp.pca.krumsiek11.h5ad"/> 1667 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
1663 <param name="format" value="png"/> 1668 <param name="format" value="png"/>
1664 <conditional name="method"> 1669 <conditional name="method">
1673 <has_text_matching expression="log=False"/> 1678 <has_text_matching expression="log=False"/>
1674 </assert_contents> 1679 </assert_contents>
1675 </output> 1680 </output>
1676 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="image_diff"/> 1681 <output name="out_png" file="pl.pca_variance_ratio.pp.pca.krumsiek11.png" compare="image_diff"/>
1677 </test> 1682 </test>
1678 1683
1679 <!-- test 21 --> 1684 <!-- test 21 -->
1680 <test expect_num_outputs="2"> 1685 <test expect_num_outputs="2">
1681 <param name="adata" value="pp.pca.krumsiek11.h5ad"/> 1686 <param name="adata" value="pp.pca.krumsiek11.h5ad"/>
1682 <param name="format" value="png"/> 1687 <param name="format" value="png"/>
1683 <conditional name="method"> 1688 <conditional name="method">
1707 <has_text_matching expression="hspace=0.25"/> 1712 <has_text_matching expression="hspace=0.25"/>
1708 </assert_contents> 1713 </assert_contents>
1709 </output> 1714 </output>
1710 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="image_diff"/> 1715 <output name="out_png" file="pl.pca_overview.pp.pca.krumsiek11.png" compare="image_diff"/>
1711 </test> 1716 </test>
1712 1717
1713 <!-- test 22 --> 1718 <!-- test 22 -->
1714 <test expect_num_outputs="2"> 1719 <test expect_num_outputs="2">
1715 <param name="adata" value="tl.tsne.krumsiek11.h5ad"/> 1720 <param name="adata" value="tl.tsne.krumsiek11.h5ad"/>
1716 <param name="format" value="png"/> 1721 <param name="format" value="png"/>
1717 <conditional name="method"> 1722 <conditional name="method">
1743 <has_text_matching expression="hspace=0.25"/> 1748 <has_text_matching expression="hspace=0.25"/>
1744 </assert_contents> 1749 </assert_contents>
1745 </output> 1750 </output>
1746 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="image_diff"/> 1751 <output name="out_png" file="pl.tsne.krumsiek11.png" ftype="png" compare="image_diff"/>
1747 </test> 1752 </test>
1748 1753
1749 <!-- test 23 --> 1754 <!-- test 23 -->
1750 <test expect_num_outputs="2"> 1755 <test expect_num_outputs="2">
1751 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/> 1756 <param name="adata" value="tl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
1752 <param name="format" value="png"/> 1757 <param name="format" value="png"/>
1753 <conditional name="method"> 1758 <conditional name="method">
1781 <has_text_matching expression="size=1.0"/> 1786 <has_text_matching expression="size=1.0"/>
1782 <has_text_matching expression="frameon=True"/> 1787 <has_text_matching expression="frameon=True"/>
1783 <has_text_matching expression="ncols=4"/> 1788 <has_text_matching expression="ncols=4"/>
1784 <has_text_matching expression="wspace=0.1"/> 1789 <has_text_matching expression="wspace=0.1"/>
1785 <has_text_matching expression="hspace=0.25"/> 1790 <has_text_matching expression="hspace=0.25"/>
1786 1791
1787 </assert_contents> 1792 </assert_contents>
1788 </output> 1793 </output>
1789 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/> 1794 <output name="out_png" file="pl.umap.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
1790 </test> 1795 </test>
1791 1796
1792 <!-- test 24 --> 1797 <!-- test 24 -->
1793 <test expect_num_outputs="2"> 1798 <test expect_num_outputs="2">
1794 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> 1799 <param name="adata" value="tl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
1795 <param name="format" value="png"/> 1800 <param name="format" value="png"/>
1796 <conditional name="method"> 1801 <conditional name="method">
1818 <has_text_matching expression="size=1.0"/> 1823 <has_text_matching expression="size=1.0"/>
1819 <has_text_matching expression="frameon=True"/> 1824 <has_text_matching expression="frameon=True"/>
1820 <has_text_matching expression="ncols=4"/> 1825 <has_text_matching expression="ncols=4"/>
1821 <has_text_matching expression="wspace=0.1"/> 1826 <has_text_matching expression="wspace=0.1"/>
1822 <has_text_matching expression="hspace=0.25"/> 1827 <has_text_matching expression="hspace=0.25"/>
1823 1828
1824 </assert_contents> 1829 </assert_contents>
1825 </output> 1830 </output>
1826 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/> 1831 <output name="out_png" file="pl.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
1827 </test> 1832 </test>
1828 1833
1829 <!-- test 25 --> 1834 <!-- test 25 -->
1830 <test expect_num_outputs="2"> 1835 <test expect_num_outputs="2">
1831 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/> 1836 <param name="adata" value="tl.draw_graph.pp.neighbors_umap_euclidean.recipe_weinreb17.paul15_subsample.h5ad"/>
1832 <param name="format" value="png"/> 1837 <param name="format" value="png"/>
1833 <conditional name="method"> 1838 <conditional name="method">
1863 <has_text_matching expression="hspace=0.25"/> 1868 <has_text_matching expression="hspace=0.25"/>
1864 </assert_contents> 1869 </assert_contents>
1865 </output> 1870 </output>
1866 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="image_diff"/> 1871 <output name="out_png" file="pl.draw_graph.png" ftype="png" compare="image_diff"/>
1867 </test> 1872 </test>
1868 1873
1869 <!-- test 26 --> 1874 <!-- test 26 -->
1870 <test expect_num_outputs="2"> 1875 <test expect_num_outputs="2">
1871 <param name="adata" value="tl.embedding_density.umap.pbmc68k_reduced.h5ad"/> 1876 <param name="adata" value="tl.embedding_density.umap.pbmc68k_reduced.h5ad"/>
1872 <param name="format" value="png"/> 1877 <param name="format" value="png"/>
1873 <conditional name="method"> 1878 <conditional name="method">
1884 <has_text_matching expression="key='umap_density_bulk_labels'"/> 1889 <has_text_matching expression="key='umap_density_bulk_labels'"/>
1885 </assert_contents> 1890 </assert_contents>
1886 </output> 1891 </output>
1887 <output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="image_diff"/> 1892 <output name="out_png" file="pl.embedding_density.pbmc68k_reduced.png" ftype="png" compare="image_diff"/>
1888 </test> 1893 </test>
1889 1894
1890 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. --> 1895 <!-- This function is commented out because it is not compatible with pandas version. If the issue is not resolved in the next update, this should be removed. -->
1891 <!-- test 27 --> 1896 <!-- test 27 -->
1892 <!-- <test expect_num_outputs="2"> 1897 <!-- <test expect_num_outputs="2">
1893 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> 1898 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
1894 <param name="format" value="png"/> 1899 <param name="format" value="png"/>
1895 <conditional name="method"> 1900 <conditional name="method">
1896 <param name="method" value="pl.dpt_groups_pseudotime"/> 1901 <param name="method" value="pl.dpt_groups_pseudotime"/>
1897 1902
1898 </conditional> 1903 </conditional>
1899 <section name="advanced_common"> 1904 <section name="advanced_common">
1900 <param name="show_log" value="true"/> 1905 <param name="show_log" value="true"/>
1901 </section> 1906 </section>
1902 <output name="hidden_output"> 1907 <output name="hidden_output">
1905 <has_text_matching expression="color_map='viridis'"/> 1910 <has_text_matching expression="color_map='viridis'"/>
1906 </assert_contents> 1911 </assert_contents>
1907 </output> 1912 </output>
1908 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/> 1913 <output name="out_png" file="pl.dpt_groups_pseudotime.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
1909 </test> --> 1914 </test> -->
1910 1915
1911 <!-- test 28 --> 1916 <!-- test 28 -->
1912 <test expect_num_outputs="2"> 1917 <test expect_num_outputs="2">
1913 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/> 1918 <param name="adata" value="tl.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.h5ad"/>
1914 <param name="format" value="png"/> 1919 <param name="format" value="png"/>
1915 <conditional name="method"> 1920 <conditional name="method">
1924 <has_text_matching expression="as_heatmap=True"/> 1929 <has_text_matching expression="as_heatmap=True"/>
1925 </assert_contents> 1930 </assert_contents>
1926 </output> 1931 </output>
1927 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/> 1932 <output name="out_png" file="pl.dpt_timeseries.dpt.diffmap.neighbors_gauss_braycurtis.recipe_weinreb17.paul15_subsample.png" ftype="png" compare="image_diff"/>
1928 </test> 1933 </test>
1929 1934
1930 <!-- test 29 --> 1935 <!-- test 29 -->
1931 <test expect_num_outputs="1"> 1936 <test expect_num_outputs="2">
1932 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/> 1937 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
1933 <param name="format" value="png"/> 1938 <param name="format" value="png"/>
1934 <conditional name="method"> 1939 <conditional name="method">
1935 <param name="method" value="pl.paga"/> 1940 <param name="method" value="pl.paga"/>
1936 <param name="threshold" value="0.01"/> 1941 <param name="threshold" value="0.01"/>
1938 <param name="layout" value="fr"/> 1943 <param name="layout" value="fr"/>
1939 <param name="fontsize" value="1"/> 1944 <param name="fontsize" value="1"/>
1940 <param name="edge_width_scale" value="5"/> 1945 <param name="edge_width_scale" value="5"/>
1941 </conditional> 1946 </conditional>
1942 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/> 1947 <output name="out_png" file="pl.paga.paul15_gauss_braycurtis.png" ftype="png" compare="image_diff"/>
1943 </test> 1948 <output name="anndata_out" ftype="h5ad">
1944 1949 <assert_contents>
1950 <has_h5_keys keys="uns/paga"/>
1951 </assert_contents>
1952 </output>
1953 </test>
1954
1945 <!-- test 30 --> 1955 <!-- test 30 -->
1946 <test expect_num_outputs="1"> 1956 <test expect_num_outputs="1">
1947 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/> 1957 <param name="adata" value="tl.paga.neighbors.paul15_gauss_braycurtis.h5ad"/>
1948 <param name="format" value="png"/> 1958 <param name="format" value="png"/>
1949 <conditional name="method"> 1959 <conditional name="method">
1959 1969
1960 <!-- test 31 --> 1970 <!-- test 31 -->
1961 <!-- <test expect_num_outputs="2"> 1971 <!-- <test expect_num_outputs="2">
1962 test pl.paga_path 1972 test pl.paga_path
1963 </test> --> 1973 </test> -->
1964 1974
1965 <!-- test 32 --> 1975 <!-- test 32 -->
1966 <test expect_num_outputs="2"> 1976 <test expect_num_outputs="2">
1967 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 1977 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
1968 <param name="format" value="png"/> 1978 <param name="format" value="png"/>
1969 <conditional name="method"> 1979 <conditional name="method">
1970 <param name="method" value="pl.rank_genes_groups"/> 1980 <param name="method" value="pl.rank_genes_groups"/>
1971 <param name="n_genes" value="10"/> 1981 <param name="n_genes" value="10"/>
1972 </conditional> 1982 </conditional>
1973 <section name="advanced_common"> 1983 <section name="advanced_common">
1974 <param name="show_log" value="true"/> 1984 <param name="show_log" value="true"/>
1975 </section> 1985 </section>
1976 <output name="hidden_output"> 1986 <output name="hidden_output">
1981 <has_text_matching expression="ncols=4"/> 1991 <has_text_matching expression="ncols=4"/>
1982 </assert_contents> 1992 </assert_contents>
1983 </output> 1993 </output>
1984 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/> 1994 <output name="out_png" file="pl.rank_genes_groups.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
1985 </test> 1995 </test>
1986 1996
1987 <!-- test 33 --> 1997 <!-- test 33 -->
1988 <test expect_num_outputs="2"> 1998 <test expect_num_outputs="2">
1989 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 1999 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
1990 <param name="format" value="png"/> 2000 <param name="format" value="png"/>
1991 <conditional name="method"> 2001 <conditional name="method">
2016 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="image_diff" eps="3.5"/> 2026 <element name="cell_type_Mo" file="pl.rank_genes_groups_violin.Mo.png" ftype="png" compare="image_diff" eps="3.5"/>
2017 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="image_diff" eps="3.5"/> 2027 <element name="cell_type_Neu" file="pl.rank_genes_groups_violin.Neu.png" ftype="png" compare="image_diff" eps="3.5"/>
2018 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="image_diff" eps="3.5"/> 2028 <element name="cell_type_progenitor" file="pl.rank_genes_groups_violin.progenitor.png" ftype="png" compare="image_diff" eps="3.5"/>
2019 </output_collection> 2029 </output_collection>
2020 </test> 2030 </test>
2021 2031
2022 <!-- test 34 --> 2032 <!-- test 34 -->
2023 <test expect_num_outputs="2"> 2033 <test expect_num_outputs="2">
2024 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 2034 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2025 <param name="format" value="png"/> 2035 <param name="format" value="png"/>
2026 <conditional name="method"> 2036 <conditional name="method">
2054 <has_text_matching expression="saturation=0.75"/> 2064 <has_text_matching expression="saturation=0.75"/>
2055 </assert_contents> 2065 </assert_contents>
2056 </output> 2066 </output>
2057 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff" eps="1.5"/> 2067 <output name="out_png" file="pl.rank_genes_groups_stacked_violin.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff" eps="1.5"/>
2058 </test> 2068 </test>
2059 2069
2060 <!-- test 35 --> 2070 <!-- test 35 -->
2061 <test expect_num_outputs="2"> 2071 <test expect_num_outputs="2">
2062 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 2072 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2063 <param name="format" value="png"/> 2073 <param name="format" value="png"/>
2064 <conditional name="method"> 2074 <conditional name="method">
2103 <has_text_matching expression="dendrogram=False"/> 2113 <has_text_matching expression="dendrogram=False"/>
2104 </assert_contents> 2114 </assert_contents>
2105 </output> 2115 </output>
2106 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/> 2116 <output name="out_png" file="pl.rank_genes_groups_dotplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
2107 </test> 2117 </test>
2108 2118
2109 <!-- test 37 --> 2119 <!-- test 37 -->
2110 <test expect_num_outputs="2"> 2120 <test expect_num_outputs="2">
2111 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/> 2121 <param name="adata" value="tl.rank_genes_groups.krumsiek11.h5ad"/>
2112 <param name="format" value="png"/> 2122 <param name="format" value="png"/>
2113 <conditional name="method"> 2123 <conditional name="method">
2128 <has_text_matching expression="snap=False"/> 2138 <has_text_matching expression="snap=False"/>
2129 </assert_contents> 2139 </assert_contents>
2130 </output> 2140 </output>
2131 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/> 2141 <output name="out_png" file="pl.rank_genes_groups_matrixplot.rank_genes_groups.krumsiek11.png" ftype="png" compare="image_diff"/>
2132 </test> 2142 </test>
2133 2143
2134 <!-- test 38 pl.rank_genes_groups_dotplot with marker list--> 2144 <!-- test 38 pl.rank_genes_groups_dotplot with marker list-->
2135 <test expect_num_outputs="2"> 2145 <test expect_num_outputs="2">
2136 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> 2146 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
2137 <param name="format" value="png"/> 2147 <param name="format" value="png"/>
2138 <conditional name="method"> 2148 <conditional name="method">
2153 <has_text_matching expression="dendrogram=False"/> 2163 <has_text_matching expression="dendrogram=False"/>
2154 </assert_contents> 2164 </assert_contents>
2155 </output> 2165 </output>
2156 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="image_diff"/> 2166 <output name="out_png" file="pl.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_marker_1.png" ftype="png" compare="image_diff"/>
2157 </test> 2167 </test>
2158 2168
2159 <!-- test 39: pl.rank_genes_groups_dotplot with marker list --> 2169 <!-- test 39: pl.rank_genes_groups_dotplot with marker list -->
2160 <test expect_num_outputs="2"> 2170 <test expect_num_outputs="2">
2161 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" /> 2171 <param name="adata" value="cosg.rank_genes_groups.newton-cg.pbmc68k_highly_reduced_1.h5ad" />
2162 <param name="format" value="png"/> 2172 <param name="format" value="png"/>
2163 <conditional name="method"> 2173 <conditional name="method">