update flexynesis cbio tool#1643
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bgruening merged 5 commits intobgruening:masterfrom Jun 26, 2025
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Thanks! yes I'm still working on the tests. |
bgruening
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Jun 25, 2025
| </collection> | ||
| <data name="report" format="html" label="${tool.name} on ${study_id}: cBioPortal validation report" from_work_dir="output/cBioPortal_validation_report.html"> | ||
| <filter>study_id in htm_studies or study_id in html_studies</filter> | ||
| <filter>study_id in ['lgg_tcga', 'cesc_tcga', 'acc_tcga_gdc', 'alal_target_gdc', 'aml_target_gdc', 'aml_tcga_gdc', 'blca_tcga_gdc', 'bll_target_gdc', 'brain_cptac_gdc', 'brca_tcga_gdc', 'breast_cptac_gdc', 'ccrcc_tcga_gdc', 'cesc_tcga_gdc', 'chol_tcga_gdc', 'chrcc_tcga_gdc', 'coad_cptac_gdc', 'coad_tcga_gdc', 'difg_tcga_gdc', 'dlbclnos_tcga_gdc', 'esca_tcga_gdc', 'gbm_tcga_gdc', 'hcc_tcga_gdc', 'hgsoc_tcga_gdc', 'hnsc_tcga_gdc', 'luad_cptac_gdc', 'luad_tcga_gdc', 'lusc_cptac_gdc', 'lusc_tcga_gdc', 'mnet_tcga_gdc', 'nbl_target_gdc', 'nsgct_tcga_gdc', 'ohnca_cptac_gdc', 'os_target_gdc', 'ovary_cptac_gdc', 'paad_tcga_gdc', 'pancreas_cptac_gdc', 'plmeso_tcga_gdc', 'prad_tcga_gdc', 'prcc_tcga_gdc', 'rcc_cptac_gdc', 'read_tcga_gdc', 'skcm_tcga_gdc', 'soft_tissue_tcga_gdc', 'stad_tcga_gdc', 'thpa_tcga_gdc', 'thym_tcga_gdc', 'ucec_tcga_gdc', 'ucs_tcga_gdc', 'uec_cptac_gdc', 'um_tcga_gdc', 'wt_target_gdc']</filter> |
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One of the tool outputs is an HTML report. The problem is that not all studies on cbioportal have this HTML report.
This update tries to fix this issue