Mercurial > repos > bgruening > flexynesis_cbioportal_import
changeset 4:9c57d6edd3c1 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
| author | bgruening |
|---|---|
| date | Mon, 30 Jun 2025 17:19:44 +0000 |
| parents | 2b414a6c35af |
| children | e9a7cb5a3c63 |
| files | flexynesis_cbioportal_import.xml macros.xml test-data/loc.sample tool-data/flexynesis.loc.sample |
| diffstat | 4 files changed, 108 insertions(+), 440 deletions(-) [+] |
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--- a/flexynesis_cbioportal_import.xml Tue Jun 24 11:33:40 2025 +0000 +++ b/flexynesis_cbioportal_import.xml Mon Jun 30 17:19:44 2025 +0000 @@ -5,13 +5,28 @@ </macros> <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ + ## list of studies with html report + #set $htm_studies = ['lgg_tcga', 'cesc_tcga'] + #set $html_studies = ['acc_tcga_gdc', 'alal_target_gdc', 'aml_target_gdc', 'aml_tcga_gdc', 'blca_tcga_gdc', + 'bll_target_gdc', 'brain_cptac_gdc', 'brca_tcga_gdc', 'breast_cptac_gdc', 'ccrcc_tcga_gdc', + 'cesc_tcga_gdc', 'chol_tcga_gdc', 'chrcc_tcga_gdc', 'coad_cptac_gdc', 'coad_tcga_gdc', + 'difg_tcga_gdc', 'dlbclnos_tcga_gdc', 'esca_tcga_gdc', 'gbm_tcga_gdc', 'hcc_tcga_gdc', + 'hgsoc_tcga_gdc', 'hnsc_tcga_gdc', 'luad_cptac_gdc', 'luad_tcga_gdc', 'lusc_cptac_gdc', + 'lusc_tcga_gdc', 'mnet_tcga_gdc', 'nbl_target_gdc', 'nsgct_tcga_gdc', 'ohnca_cptac_gdc', + 'os_target_gdc', 'ovary_cptac_gdc', 'paad_tcga_gdc', 'pancreas_cptac_gdc', 'plmeso_tcga_gdc', + 'prad_tcga_gdc', 'prcc_tcga_gdc', 'rcc_cptac_gdc', 'read_tcga_gdc', 'skcm_tcga_gdc', + 'soft_tissue_tcga_gdc', 'stad_tcga_gdc', 'thpa_tcga_gdc', 'thym_tcga_gdc', 'ucec_tcga_gdc', + 'ucs_tcga_gdc', 'uec_cptac_gdc', 'um_tcga_gdc', 'wt_target_gdc'] @CHECK_NON_COMMERCIAL_USE@ mkdir -p output/data output/meta && python '$cbio_config' && - cat cbioportal_data.txt && mv $str($study_id)/data* output/data/ && mv $str($study_id)/meta* output/meta/ && - mv $str($study_id)/*.htm output/cBioPortal_validation_report.html && + #if $study_id in $htm_studies: + mv $str($study_id)/*.htm output/cBioPortal_validation_report.html && + #else if $study_id in $html_studies: + mv $str($study_id)/validation_reports/*validation.html output/cBioPortal_validation_report.html && + #end if cd output/data && for file in *; do if [[ -f \$file ]]; then mv "\$file" "\${file%.txt}.tabular"; fi; done ]]></command> @@ -22,11 +37,6 @@ cbioportal = CBioPortalData(study_id='$study_id') cbioportal.get_cbioportal_data(study_id='$study_id') - -output_path = f"cbioportal_data.txt" -with open(output_path, 'w') as f: - with redirect_stdout(f): - cbioportal.get_cbioportal_data('lgg_tcga') ]]></configfile> </configfiles> <inputs> @@ -44,9 +54,18 @@ <collection name="meta" type="list" label="${tool.name} on ${study_id}: metadata"> <discover_datasets pattern="__name_and_ext__" format="tabular" directory="output/meta"/> </collection> - <data name="report" format="html" label="${tool.name} on ${study_id}: cBioPortal validation report" from_work_dir="output/cBioPortal_validation_report.html"/> + <data name="report" format="html" label="${tool.name} on ${study_id}: cBioPortal validation report" from_work_dir="output/cBioPortal_validation_report.html"> + <!-- note about the filter here: + Not all studies in the cbioportal datahub have html reports. + The main repository can be find here: https://github.com/cBioPortal/datahub/ + Two studies in https://github.com/cBioPortal/datahub/tree/master/public have html reports (as .htm files), + and studies in crdc here: https://github.com/cBioPortal/datahub/tree/master/crdc have html reports + So from 479 studies only 51 have this report. --> + <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> + </data> </outputs> <tests> + <!-- test 1: html report public--> <test expect_num_outputs="3"> <param name="non_commercial_use" value="True"/> <param name="study_id" value="lgg_tcga"/> @@ -84,6 +103,77 @@ </assert_contents> </output> </test> + <!-- test 2: html report crdc--> + <test expect_num_outputs="3"> + <param name="non_commercial_use" value="True"/> + <param name="study_id" value="acc_tcga_gdc"/> + <output_collection name="data" type="list" count="14"> + <element name="data_clinical_patient"> + <assert_contents> + <has_text_matching expression="PATIENT_ID"/> + <has_n_lines n="97"/> + </assert_contents> + </element> + <element name="data_cna"> + <assert_contents> + <has_text_matching expression="Entrez_Gene_Id"/> + <has_n_lines n="38322"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="meta" type="list" count="15"> + <element name="meta_clinical_patient"> + <assert_contents> + <has_text_matching expression="cancer_study_identifier: acc_tcga_gdc"/> + <has_n_lines n="4"/> + </assert_contents> + </element> + <element name="meta_cna"> + <assert_contents> + <has_text_matching expression="data_filename: data_cna.txt"/> + <has_n_lines n="8"/> + </assert_contents> + </element> + </output_collection> + <output name="report"> + <assert_contents> + <has_text_matching expression="cBioPortal validation report"/> + </assert_contents> + </output> + </test> + <!-- test 3: no report --> + <test expect_num_outputs="2"> + <param name="non_commercial_use" value="True"/> + <param name="study_id" value="acc_2019"/> + <output_collection name="data" type="list" count="8"> + <element name="data_clinical_patient"> + <assert_contents> + <has_text_matching expression="PATIENT_ID"/> + <has_n_lines n="1050"/> + </assert_contents> + </element> + <element name="data_cna"> + <assert_contents> + <has_text_matching expression="Hugo_Symbol"/> + <has_n_lines n="21673"/> + </assert_contents> + </element> + </output_collection> + <output_collection name="meta" type="list" count="9"> + <element name="meta_clinical_patient"> + <assert_contents> + <has_text_matching expression="cancer_study_identifier:acc_2019"/> + <has_n_lines n="4"/> + </assert_contents> + </element> + <element name="meta_cna"> + <assert_contents> + <has_text_matching expression="data_filename: data_cna.txt"/> + <has_n_lines n="8"/> + </assert_contents> + </element> + </output_collection> + </test> </tests> <help><![CDATA[ @COMMON_HELP@ @@ -98,10 +188,16 @@ **Outputs** -Two collections of data and metadata datasets and an additional html report. +Two collections of data and metadata datasets and an additional html report (if available). + + +The available datasets can be checked from here_ + +If the study ID is not available, please contact the administrator of this Galaxy instance. .. _Documentation: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/ .. _copyright holders: https://github.com/BIMSBbioinfo/flexynesis +.. _here: https://github.com/cBioPortal/datahub/ ]]></help> <expand macro="creator"> <person givenName="Polina" familyName="Polunina" email="polunina@informatik.uni-freiburg.de"/>
--- a/macros.xml Tue Jun 24 11:33:40 2025 +0000 +++ b/macros.xml Mon Jun 30 17:19:44 2025 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">0.2.20</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">24.1</token> <xml name="requirements"> <requirements>
--- a/test-data/loc.sample Tue Jun 24 11:33:40 2025 +0000 +++ b/test-data/loc.sample Mon Jun 30 17:19:44 2025 +0000 @@ -1,1 +1,3 @@ lgg_tcga lgg_tcga 1 +acc_tcga_gdc acc_tcga_gdc 1 +acc_2019 acc_2019 1 \ No newline at end of file
--- a/tool-data/flexynesis.loc.sample Tue Jun 24 11:33:40 2025 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,430 +0,0 @@ -acbc_mskcc_2015 acbc_mskcc_2015 1 -acc_2019 acc_2019 1 -acc_tcga acc_tcga 1 -acc_tcga_pan_can_atlas_2018 acc_tcga_pan_can_atlas_2018 1 -acyc_fmi_2014 acyc_fmi_2014 1 -acyc_jhu_2016 acyc_jhu_2016 1 -acyc_mda_2015 acyc_mda_2015 1 -acyc_mgh_2016 acyc_mgh_2016 1 -acyc_mskcc_2013 acyc_mskcc_2013 1 -acyc_sanger_2013 acyc_sanger_2013 1 -aflexynesis.loc aflexynesis.loc 1 -all_phase2_target_2018_pub all_phase2_target_2018_pub 1 -all_stjude_2013 all_stjude_2013 1 -all_stjude_2015 all_stjude_2015 1 -all_stjude_2016 all_stjude_2016 1 -aml_ohsu_2018 aml_ohsu_2018 1 -aml_ohsu_2022 aml_ohsu_2022 1 -aml_target_2018_pub aml_target_2018_pub 1 -ampca_bcm_2016 ampca_bcm_2016 1 -angs_painter_2020 angs_painter_2020 1 -angs_project_painter_2018 angs_project_painter_2018 1 -appendiceal_msk_2022 appendiceal_msk_2022 1 -asclc_msk_2024 asclc_msk_2024 1 -bcc_unige_2016 bcc_unige_2016 1 -bfn_duke_nus_2015 bfn_duke_nus_2015 1 -biliary_tract_summit_2022 biliary_tract_summit_2022 1 -bladder_columbia_msk_2018 bladder_columbia_msk_2018 1 -bladder_msk_2023 bladder_msk_2023 1 -blca_bcan_hcrn_2022 blca_bcan_hcrn_2022 1 -blca_bgi blca_bgi 1 -blca_cornell_2016 blca_cornell_2016 1 -blca_dfarber_mskcc_2014 blca_dfarber_mskcc_2014 1 -blca_mskcc_solit_2012 blca_mskcc_solit_2012 1 -blca_mskcc_solit_2014 blca_mskcc_solit_2014 1 -blca_msk_tcga_2020 blca_msk_tcga_2020 1 -blca_nmibc_2017 blca_nmibc_2017 1 -blca_plasmacytoid_mskcc_2016 blca_plasmacytoid_mskcc_2016 1 -blca_tcga blca_tcga 1 -blca_tcga_pan_can_atlas_2018 blca_tcga_pan_can_atlas_2018 1 -blca_tcga_pub blca_tcga_pub 1 -blca_tcga_pub_2017 blca_tcga_pub_2017 1 -bm_nsclc_mskcc_2023 bm_nsclc_mskcc_2023 1 -bowel_colitis_msk_2022 bowel_colitis_msk_2022 1 -braf_msk_archer_2024 braf_msk_archer_2024 1 -braf_msk_impact_2024 braf_msk_impact_2024 1 -brain_cptac_2020 brain_cptac_2020 1 -brca_bccrc brca_bccrc 1 -brca_bccrc_xenograft_2014 brca_bccrc_xenograft_2014 1 -brca_broad brca_broad 1 -brca_cptac_2020 brca_cptac_2020 1 -brca_dfci_2020 brca_dfci_2020 1 -brca_fuscc_2020 brca_fuscc_2020 1 -brca_hta9_htan_2022 brca_hta9_htan_2022 1 -brca_igr_2015 brca_igr_2015 1 -brca_jup_msk_2020 brca_jup_msk_2020 1 -brca_mapk_hp_msk_2021 brca_mapk_hp_msk_2021 1 -brca_mbcproject_2022 brca_mbcproject_2022 1 -brca_mbcproject_wagle_2017 brca_mbcproject_wagle_2017 1 -brca_metabric brca_metabric 1 -brca_mskcc_2019 brca_mskcc_2019 1 -brca_pareja_msk_2020 brca_pareja_msk_2020 1 -brca_sanger brca_sanger 1 -brca_smc_2018 brca_smc_2018 1 -brca_tcga brca_tcga 1 -brca_tcga_pan_can_atlas_2018 brca_tcga_pan_can_atlas_2018 1 -brca_tcga_pub brca_tcga_pub 1 -brca_tcga_pub2015 brca_tcga_pub2015 1 -breast_alpelisib_2020 breast_alpelisib_2020 1 -breast_ink4_msk_2021 breast_ink4_msk_2021 1 -breast_msk_2018 breast_msk_2018 1 -ccle_broad_2019 ccle_broad_2019 1 -ccrcc_dfci_2019 ccrcc_dfci_2019 1 -ccrcc_irc_2014 ccrcc_irc_2014 1 -ccrcc_utokyo_2013 ccrcc_utokyo_2013 1 -cellline_ccle_broad cellline_ccle_broad 1 -cellline_nci60 cellline_nci60 1 -cervix_msk_2023 cervix_msk_2023 1 -cesc_tcga cesc_tcga 1 -cesc_tcga_pan_can_atlas_2018 cesc_tcga_pan_can_atlas_2018 1 -cfdna_msk_2019 cfdna_msk_2019 1 -chl_sccc_2023 chl_sccc_2023 1 -chol_icgc_2017 chol_icgc_2017 1 -chol_jhu_2013 chol_jhu_2013 1 -chol_msk_2018 chol_msk_2018 1 -chol_nccs_2013 chol_nccs_2013 1 -chol_nus_2012 chol_nus_2012 1 -chol_tcga chol_tcga 1 -chol_tcga_pan_can_atlas_2018 chol_tcga_pan_can_atlas_2018 1 -cll_broad_2015 cll_broad_2015 1 -cll_broad_2022 cll_broad_2022 1 -cll_iuopa_2015 cll_iuopa_2015 1 -cllsll_icgc_2011 cllsll_icgc_2011 1 -coad_caseccc_2015 coad_caseccc_2015 1 -coad_cptac_2019 coad_cptac_2019 1 -coadread_cass_2020 coadread_cass_2020 1 -coadread_dfci_2016 coadread_dfci_2016 1 -coadread_genentech coadread_genentech 1 -coadread_mskcc coadread_mskcc 1 -coadread_mskresistance_2022 coadread_mskresistance_2022 1 -coadread_tcga coadread_tcga 1 -coadread_tcga_pan_can_atlas_2018 coadread_tcga_pan_can_atlas_2018 1 -coadread_tcga_pub coadread_tcga_pub 1 -coad_silu_2022 coad_silu_2022 1 -crc_apc_impact_2020 crc_apc_impact_2020 1 -crc_dd_2022 crc_dd_2022 1 -crc_eo_2020 crc_eo_2020 1 -crc_hta11_htan_2021 crc_hta11_htan_2021 1 -crc_msk_2017 crc_msk_2017 1 -crc_nigerian_2020 crc_nigerian_2020 1 -cscc_dfarber_2015 cscc_dfarber_2015 1 -cscc_hgsc_bcm_2014 cscc_hgsc_bcm_2014 1 -cscc_ranson_2022 cscc_ranson_2022 1 -cscc_ucsf_2021 cscc_ucsf_2021 1 -csf_msk_2024 csf_msk_2024 1 -ctcl_columbia_2015 ctcl_columbia_2015 1 -desm_broad_2015 desm_broad_2015 1 -difg_glass difg_glass 1 -difg_glass_2019 difg_glass_2019 1 -difg_msk_2023 difg_msk_2023 1 -dlbc_broad_2012 dlbc_broad_2012 1 -dlbcl_dfci_2018 dlbcl_dfci_2018 1 -dlbcl_duke_2017 dlbcl_duke_2017 1 -dlbc_tcga dlbc_tcga 1 -dlbc_tcga_pan_can_atlas_2018 dlbc_tcga_pan_can_atlas_2018 1 -egc_msk_2017 egc_msk_2017 1 -egc_msk_2023 egc_msk_2023 1 -egc_mskcc_2020 egc_mskcc_2020 1 -egc_msk_tp53_ccr_2022 egc_msk_tp53_ccr_2022 1 -egc_tmucih_2015 egc_tmucih_2015 1 -egc_trap_ccr_msk_2023 egc_trap_ccr_msk_2023 1 -egc_trap_msk_2020 egc_trap_msk_2020 1 -esca_broad esca_broad 1 -esca_tcga esca_tcga 1 -esca_tcga_pan_can_atlas_2018 esca_tcga_pan_can_atlas_2018 1 -escc_icgc escc_icgc 1 -escc_ucla_2014 escc_ucla_2014 1 -es_dfarber_broad_2014 es_dfarber_broad_2014 1 -es_dsrct_msk_2023 es_dsrct_msk_2023 1 -es_iocurie_2014 es_iocurie_2014 1 -gbc_msk_2018 gbc_msk_2018 1 -gbc_mskcc_2022 gbc_mskcc_2022 1 -gbc_shanghai_2014 gbc_shanghai_2014 1 -gbm_columbia_2019 gbm_columbia_2019 1 -gbm_cptac_2021 gbm_cptac_2021 1 -gbm_mayo_pdx_sarkaria_2019 gbm_mayo_pdx_sarkaria_2019 1 -gbm_tcga gbm_tcga 1 -gbm_tcga_pan_can_atlas_2018 gbm_tcga_pan_can_atlas_2018 1 -gbm_tcga_pub gbm_tcga_pub 1 -gbm_tcga_pub2013 gbm_tcga_pub2013 1 -gct_msk_2016 gct_msk_2016 1 -gct_msk_2020 gct_msk_2020 1 -gist_msk_2022 gist_msk_2022 1 -gist_msk_2023 gist_msk_2023 1 -glioma_msk_2018 glioma_msk_2018 1 -glioma_mskcc_2019 glioma_mskcc_2019 1 -hcc_clca_2024 hcc_clca_2024 1 -hccihch_pku_2019 hccihch_pku_2019 1 -hcc_inserm_fr_2015 hcc_inserm_fr_2015 1 -hcc_jcopo_msk_2023 hcc_jcopo_msk_2023 1 -hcc_meric_2021 hcc_meric_2021 1 -hcc_msk_2024 hcc_msk_2024 1 -hcc_mskimpact_2018 hcc_mskimpact_2018 1 -hcc_msk_venturaa_2018 hcc_msk_venturaa_2018 1 -heme_msk_impact_2022 heme_msk_impact_2022 1 -hgsoc_msk_2021 hgsoc_msk_2021 1 -histiocytosis_cobi_msk_2019 histiocytosis_cobi_msk_2019 1 -hnc_mskcc_2016 hnc_mskcc_2016 1 -hnsc_broad hnsc_broad 1 -hnsc_jhu hnsc_jhu 1 -hnsc_mdanderson_2013 hnsc_mdanderson_2013 1 -hnsc_tcga hnsc_tcga 1 -hnsc_tcga_pan_can_atlas_2018 hnsc_tcga_pan_can_atlas_2018 1 -hnsc_tcga_pub hnsc_tcga_pub 1 -ihch_ismms_2015 ihch_ismms_2015 1 -ihch_msk_2021 ihch_msk_2021 1 -ihch_mskcc_2020 ihch_mskcc_2020 1 -ihch_smmu_2014 ihch_smmu_2014 1 -ilc_msk_2023 ilc_msk_2023 1 -kich_tcga kich_tcga 1 -kich_tcga_pan_can_atlas_2018 kich_tcga_pan_can_atlas_2018 1 -kich_tcga_pub kich_tcga_pub 1 -kirc_bgi kirc_bgi 1 -kirc_tcga kirc_tcga 1 -kirc_tcga_pan_can_atlas_2018 kirc_tcga_pan_can_atlas_2018 1 -kirc_tcga_pub kirc_tcga_pub 1 -kirp_tcga kirp_tcga 1 -kirp_tcga_pan_can_atlas_2018 kirp_tcga_pan_can_atlas_2018 1 -laml_tcga laml_tcga 1 -laml_tcga_pan_can_atlas_2018 laml_tcga_pan_can_atlas_2018 1 -laml_tcga_pub laml_tcga_pub 1 -lcll_broad_2013 lcll_broad_2013 1 -lgggbm_tcga_pub lgggbm_tcga_pub 1 -lgg_tcga lgg_tcga 1 -lgg_tcga_pan_can_atlas_2018 lgg_tcga_pan_can_atlas_2018 1 -lgg_ucsf_2014 lgg_ucsf_2014 1 -lgsoc_mapk_msk_2022 lgsoc_mapk_msk_2022 1 -liad_inserm_fr_2014 liad_inserm_fr_2014 1 -lihc_amc_prv lihc_amc_prv 1 -lihc_riken lihc_riken 1 -lihc_tcga lihc_tcga 1 -lihc_tcga_pan_can_atlas_2018 lihc_tcga_pan_can_atlas_2018 1 -luad_broad luad_broad 1 -luad_cptac_2020 luad_cptac_2020 1 -luad_mskcc_2015 luad_mskcc_2015 1 -luad_mskcc_2020 luad_mskcc_2020 1 -luad_mskcc_2023_met_organotropism luad_mskcc_2023_met_organotropism 1 -luad_mskimpact_2021 luad_mskimpact_2021 1 -luad_msk_npjpo_2021 luad_msk_npjpo_2021 1 -luad_oncosg_2020 luad_oncosg_2020 1 -luad_tcga luad_tcga 1 -luad_tcga_pan_can_atlas_2018 luad_tcga_pan_can_atlas_2018 1 -luad_tcga_pub luad_tcga_pub 1 -luad_tsp luad_tsp 1 -lung_msk_2017 lung_msk_2017 1 -lung_msk_mind_2020 lung_msk_mind_2020 1 -lung_msk_pdx lung_msk_pdx 1 -lung_nci_2022 lung_nci_2022 1 -lung_pdx_msk_2021 lung_pdx_msk_2021 1 -lung_smc_2016 lung_smc_2016 1 -lusc_cptac_2021 lusc_cptac_2021 1 -lusc_tcga lusc_tcga 1 -lusc_tcga_pan_can_atlas_2018 lusc_tcga_pan_can_atlas_2018 1 -lusc_tcga_pub lusc_tcga_pub 1 -lymphoma_cellline_msk_2020 lymphoma_cellline_msk_2020 1 -makeanimpact_ccr_2023 makeanimpact_ccr_2023 1 -mbc_msk_2021 mbc_msk_2021 1 -mbl_broad_2012 mbl_broad_2012 1 -mbl_dkfz_2017 mbl_dkfz_2017 1 -mbl_icgc mbl_icgc 1 -mbl_pcgp mbl_pcgp 1 -mbl_sickkids_2016 mbl_sickkids_2016 1 -mbn_mdacc_2013 mbn_mdacc_2013 1 -mbn_msk_2024 mbn_msk_2024 1 -mbn_sfu_2023 mbn_sfu_2023 1 -mcl_idibips_2013 mcl_idibips_2013 1 -mds_iwg_2022 mds_iwg_2022 1 -mds_mskcc_2020 mds_mskcc_2020 1 -mds_tokyo_2011 mds_tokyo_2011 1 -mel_dfci_2019 mel_dfci_2019 1 -mel_mskimpact_2020 mel_mskimpact_2020 1 -mel_tsam_liang_2017 mel_tsam_liang_2017 1 -mel_ucla_2016 mel_ucla_2016 1 -meso_tcga meso_tcga 1 -meso_tcga_pan_can_atlas_2018 meso_tcga_pan_can_atlas_2018 1 -metastatic_solid_tumors_mich_2017 metastatic_solid_tumors_mich_2017 1 -mixed_allen_2018 mixed_allen_2018 1 -mixed_cfdna_msk_2020 mixed_cfdna_msk_2020 1 -mixed_impact_subset_2022 mixed_impact_subset_2022 1 -mixed_kunga_msk_2022 mixed_kunga_msk_2022 1 -mixed_msk_tcga_2021 mixed_msk_tcga_2021 1 -mixed_pipseq_2017 mixed_pipseq_2017 1 -mixed_selpercatinib_2020 mixed_selpercatinib_2020 1 -mm_broad mm_broad 1 -mng_utoronto_2021 mng_utoronto_2021 1 -mnm_washu_2016 mnm_washu_2016 1 -mpcproject_broad_2021 mpcproject_broad_2021 1 -mpn_cimr_2013 mpn_cimr_2013 1 -mpnst_mskcc mpnst_mskcc 1 -mrt_bcgsc_2016 mrt_bcgsc_2016 1 -msk_access_2021 msk_access_2021 1 -msk_ch_2020 msk_ch_2020 1 -msk_ch_2023 msk_ch_2023 1 -msk_chord_2024 msk_chord_2024 1 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