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comparison macros.xml @ 20:387671174a49 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy commit 732303de9670376c88e7afb2f23336ee1433e97d
author iuc
date Thu, 26 Mar 2026 12:48:53 +0000
parents fc222791d03c
children
comparison
equal deleted inserted replaced
19:fc222791d03c 20:387671174a49
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.10.2</token> 2 <token name="@TOOL_VERSION@">1.11.5</token>
3 <token name="@VERSION_SUFFIX@">3</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">21.09</token> 4 <token name="@PROFILE@">21.09</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
8 <requirement type="package" version="0.10.3">anndata</requirement> 8 <requirement type="package" version="0.11.4">anndata</requirement>
9 <requirement type="package" version="1.26.4">numpy</requirement> 9 <requirement type="package" version="0.4">fa2_modified</requirement>
10 <requirement type="package" version="2.2.2">pandas</requirement>
11 <requirement type="package" version="1.14.1">scipy</requirement>
12 <requirement type="package" version="0.14.2">statsmodels</requirement>
13 <requirement type="package" version="0.3.5">fa2</requirement>
14 <yield /> 10 <yield />
15 </requirements> 11 </requirements>
16 </xml> 12 </xml>
17 <xml name="bio_tools"> 13 <xml name="bio_tools">
18 <xrefs> 14 <xrefs>
25 </creator> 21 </creator>
26 </xml> 22 </xml>
27 <xml name="citations"> 23 <xml name="citations">
28 <citations> 24 <citations>
29 <citation type="doi">10.1186/s13059-017-1382-0</citation> 25 <citation type="doi">10.1186/s13059-017-1382-0</citation>
26 <citation type="doi">10.1016/j.xgen.2025.101005</citation>
30 <citation type="doi">10.1093/gigascience/giaa102</citation> 27 <citation type="doi">10.1093/gigascience/giaa102</citation>
31 </citations> 28 </citations>
32 </xml> 29 </xml>
33
34 30
35 <!-- param macros --> 31 <!-- param macros -->
36 <xml name="sanitize_query" token_validinitial="string.printable"> 32 <xml name="sanitize_query" token_validinitial="string.printable">
37 <sanitizer> 33 <sanitizer>
38 <valid initial="@VALIDINITIAL@"> 34 <valid initial="@VALIDINITIAL@">
564 <!-- ln -s doesn't work here because the output is overwritten to the same file --> 560 <!-- ln -s doesn't work here because the output is overwritten to the same file -->
565 <token name="@CMD@"><![CDATA[ 561 <token name="@CMD@"><![CDATA[
566 cp '$adata' 'anndata.h5ad' && 562 cp '$adata' 'anndata.h5ad' &&
567 cat '$script_file' > '$hidden_output' && 563 cat '$script_file' > '$hidden_output' &&
568 python '$script_file' >> '$hidden_output' && 564 python '$script_file' >> '$hidden_output' &&
569 ls . >> '$hidden_output' &&
570 touch 'anndata_info.txt' && 565 touch 'anndata_info.txt' &&
571 cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@ 566 cat 'anndata_info.txt' @CMD_PRETTIFY_STDOUT@
572 ]]> 567 ]]>
573 </token> 568 </token>
574 <token name="@CMD_IMPORTS@"><![CDATA[ 569 <token name="@CMD_IMPORTS@"><![CDATA[
1449 #end if 1444 #end if
1450 outline_width=($method.outline_width_border, $method.outline_width_gap), 1445 outline_width=($method.outline_width_border, $method.outline_width_gap),
1451 ]]> 1446 ]]>
1452 </token> 1447 </token>
1453 1448
1454 1449 <xml name="param_interactive_plot">
1450 <param name="interactive_plot" type="boolean" checked="false" label="Make an interactive plot?" help="Creates a vitessce configuration file using easy_vitessce for interactive visualization"/>
1451 </xml>
1452
1453 <token name="@VITESSCE_ACTIVATE@"><![CDATA[
1454 import easy_vitessce as ev
1455 ev.configure_plots(enable_plots=["pca", "umap", "tsne", "diffmap", "violin", "embedding", "dotplot", "heatmap"])
1456 ev.config.update({"data": {"anndata_format": "h5ad"}})
1457 ev.config.update({"data": {"out_dir": "."}})
1458 ev.register_data_path(adata, 'anndata.h5ad')
1459 ]]>
1460 </token>
1461 <token name="@VITESSCE_CONFIG@"><![CDATA[
1462 import json
1463 ## while testing locally check galaxy_infrastructure_url is whether http://localhost:8080 or http://127.0.0.1:8080
1464 ## use the correct URL to access datasets via Galaxy API
1465 galaxy_url = "${__app__.config.galaxy_infrastructure_url}"
1466 anndata_out_id = "${__app__.security.encode_id($anndata_out.id)}"
1467 anndata_config_id = "${__app__.security.encode_id($anndata_config.id)}"
1468
1469 ## vitessce_widget is returned from sc.pl when the interactive_plot parameter is set to True
1470 config_dict = vitessce_widget.config.to_dict(base_url="")
1471 for dataset in config_dict.get('datasets', []):
1472 for file in dataset.get('files', []):
1473 if 'url' in file:
1474 file['url'] = f"{galaxy_url}/api/datasets/{anndata_out_id}/display"
1475 if 'options' in file and 'refSpecUrl' in file['options']:
1476 file['options']['refSpecUrl'] = f"{galaxy_url}/api/datasets/{anndata_config_id}/display"
1477
1478 config_js_content = f"""
1479 export const config = {json.dumps(config_dict, indent=2)};
1480 """
1481
1482 with open("config.js", "w") as f:
1483 f.write(config_js_content)
1484
1485 with open("config.json", "w") as f:
1486 json.dump(config_dict, f, indent=2)
1487 ]]>
1488 </token>
1455 <!-- unused macros --> 1489 <!-- unused macros -->
1456 <!-- <xml name="param_right_margin"> 1490 <!-- <xml name="param_right_margin">
1457 <param argument="right_margin" type="float" value="1" label="Width of the space right of each plotting panel"/> 1491 <param argument="right_margin" type="float" value="1" label="Width of the space right of each plotting panel"/>
1458 </xml> 1492 </xml>
1459 <xml name="param_left_margin"> 1493 <xml name="param_left_margin">