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Commit message:
planemo upload commit be6697efd85eddd5b79aad6219d81ed820ba83a9 |
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modified:
macros.xml rgreat.xml |
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added:
upload_data.py |
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removed:
macros_no_duplicates.xml |
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| diff -r b6089425744d -r 5bf47c3cc3b9 macros.xml --- a/macros.xml Wed Nov 13 10:08:45 2024 +0000 +++ b/macros.xml Wed Nov 13 15:17:44 2024 +0000 |
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| b'@@ -1,729 +1,2 @@\n-<macros>\n- <xml name="biomart">\n- <option value="aastaci_eg_gene">Saccharomyces pastorianus</option>\n- <option value="aclavatus_eg_gene">Aspergillus clavatus NRRL 1</option>\n- <option value="aflavus_eg_gene">Aspergillus flavus NRRL3357</option>\n- <option value="afumigatus_eg_gene">Aspergillus fumigatus Af293</option>\n- <option value="afumigatusa1163_eg_gene">Aspergillus fumigatus A1163</option>\n- <option value="agossypii_eg_gene">Ashbya gossypii</option>\n- <option value="ainvadans_eg_gene">Talaromyces marneffei</option>\n- <option value="anidulans_eg_gene">Aspergillus nidulans</option>\n- <option value="aniger_eg_gene">Aspergillus niger</option>\n- <option value="aoryzae_eg_gene">Aspergillus oryzae RIB40</option>\n- <option value="aterreus_eg_gene">Aspergillus terreus NIH2624</option>\n- <option value="bbassiana_eg_gene">Beauveria bassiana</option>\n- <option value="bcinerea_eg_gene">Botrytis cinerea B05.10</option>\n- <option value="bgraminis_eg_gene">Blumeria graminis</option>\n- <option value="calbicans_eg_gene">Candida albicans</option>\n- <option value="cauris_eg_gene">Candida auris</option>\n- <option value="cduobushaemulonis_eg_gene">Candida duobushaemulonis</option>\n- <option value="cglabrata_eg_gene">Candida glabrata</option>\n- <option value="cgloeosporioides_eg_gene">Colletotrichum gloeosporioides Cg-14</option>\n- <option value="cgraminicola_eg_gene">Colletotrichum graminicola</option>\n- <option value="chaemuloni_eg_gene">[Candida] haemuloni</option>\n- <option value="chigginsianum_eg_gene">Colletotrichum higginsianum</option>\n- <option value="cneoformans_eg_gene">Cryptococcus neoformans var. neoformans JEC21</option>\n- <option value="corbiculare_eg_gene">Colletotrichum orbiculare</option>\n- <option value="cparapsilosis_eg_gene">Candida parapsilosis</option>\n- <option value="cpseudohaemulonis_eg_gene">[Candida] pseudohaemulonii</option>\n- <option value="ctropicalis_eg_gene">Candida tropicalis</option>\n- <option value="dseptosporum_eg_gene">Dothistroma septosporum</option>\n- <option value="fculmorum_eg_gene">Fusarium culmorum UK99</option>\n- <option value="ffujikuroi_eg_gene">Fusarium fujikuroi</option>\n- <option value="fgraminearum_eg_gene">Fusarium graminearum str. PH-1</option>\n- <option value="foxysporum_eg_gene">Fusarium oxysporum</option>\n- <option value="fpseudograminearum_eg_gene">Fusarium graminearum</option>\n- <option value="fsolani_eg_gene">Fusarium solani</option>\n- <option value="fverticillioides_eg_gene">Fusarium verticillioides</option>\n- <option value="ggraminis_eg_gene">Gaeumannomyces tritici R3-111a-1</option>\n- <option value="gultimum_eg_gene">Sporisorium reilianum</option>\n- <option value="hcapsulatum_eg_gene">Histoplasma capsulatum</option>\n- <option value="kpastoris_eg_gene">Komagataella pastoris</option>\n- <option value="lmaculans_eg_gene">Leptosphaeria maculans</option>\n- <option value="mlaricipopulina_eg_gene">Melampsora larici-populina</option>\n- <option value="moryzae_eg_gene">Magnaporthe oryzae</option>\n- <option value="mpoae_eg_gene">Magnaporthe poae</option>\n- <option value="mviolaceum_eg_gene">Microbotryum violaceum</option>\n- <option value="ncrassa_eg_gene">Neurospora crassa</option>\n- <option value="nfischeri_eg_gene">Aspergillus fischeri NRRL 181</option>\n- <option value="pchrysosporium_eg_gene">Phanerochaete chrysosporium</option>\n- <option value="pgraminis_eg_gene">Puccinia graminis</option>\n- <option value="pgraminisug99_eg_gene">Puccinia graminis Ug99</option>\n- <option value="pnodorum_eg_gene">Phaeosphaeria nodorum</option>\n- <option value="poryzae_eg_gene">Magnaporthe oryzae</option>\n- <option value="pstriifor'..b'ey_eg_gene">Triticum aestivum Stanley genes (PGSBv2.2_Stanley)</option><option value="taweebil_eg_gene">Triticum aestivum Weebill genes (EI_WeebilV1)</option><option value="tcacao_eg_gene">Theobroma cacao Matina 1-6 genes (Theobroma_cacao_20110822)</option><option value="tccriollo_eg_gene">Theobroma cacao Belizian Criollo B97-61/B2 genes (Criollo_cocoa_genome_V2)</option><option value="tdicoccoides_eg_gene">Triticum dicoccoides genes (WEWSeq v.1.0)</option><option value="tpratense_eg_gene">Trifolium pratense genes (Trpr)</option><option value="tspelta_eg_gene">Triticum spelta genes (PGSBv2.0_Spelta)</option><option value="tturgidum_eg_gene">Triticum turgidum genes (svevo)</option><option value="turartu_eg_gene">Triticum urartu genes (Tu2.0)</option><option value="vangularis_eg_gene">Vigna angularis genes (Vigan1.1)</option><option value="vradiata_eg_gene">Vigna radiata genes (Vradiata_ver6)</option><option value="vunguiculata_eg_gene">Vigna unguiculata genes (ASM411807v1)</option><option value="vvinifera_eg_gene">Vitis vinifera genes (PN40024.v4)</option><option value="zmays_eg_gene">Zea mays genes (Zm-B73-REFERENCE-NAM-5.0)</option><option value="alaibachii_eg_gene">Albugo laibachii genes (ENA 1)</option><option value="bnatans_eg_gene">Bigelowiella natans genes (Bigna1)</option><option value="ddiscoideum_eg_gene">Dictyostelium discoideum genes (dicty_2.7)</option><option value="ehistolytica_eg_gene">Entamoeba histolytica genes (JCVI-ESG2-1.0)</option><option value="ehuxleyi_eg_gene">Emiliania huxleyi genes (Emiliana huxleyi CCMP1516 main genome assembly v1.0)</option><option value="glamblia_eg_gene">Giardia lamblia genes (GL2)</option><option value="gtheta_eg_gene">Guillardia theta CCMP2712 genes (Guith1)</option><option value="harabidopsidis_eg_gene">Hyaloperonospora arabidopsidis genes (HyaAraEmoy2_2.0)</option><option value="lmajor_eg_gene">Leishmania major genes (ASM272v2)</option><option value="paphanidermatum_eg_gene">Pythium aphanidermatum genes (pag1_scaffolds_v1)</option><option value="parrhenomanes_eg_gene">Pythium arrhenomanes genes (par_scaffolds_v1)</option><option value="pberghei_eg_gene">Plasmodium berghei genes (PBANKA01)</option><option value="pchabaudi_eg_gene">Plasmodium chabaudi genes (PCHAS01)</option><option value="pfalciparum_eg_gene">Plasmodium falciparum 3D7 genes (ASM276v2)</option><option value="pinfestans_eg_gene">Phytophthora infestans genes (ASM14294v1)</option><option value="pirregulare_eg_gene">Pythium irregulare genes (pir_scaffolds_v1)</option><option value="piwayamai_eg_gene">Pythium iwayamai genes (piw_scaffolds_v1)</option><option value="pkernoviae_eg_gene">Phytophthora kernoviae genes (PhyKer238/432v1)</option><option value="pknowlesi_eg_gene">Plasmodium knowlesi genes (ASM635v1)</option><option value="plateralis_eg_gene">Phytophthora lateralis genes (MPF4_v1.0)</option><option value="pmultistriata_eg_gene">Pseudo-nitzschia multistriata genes (ASM90066040v1)</option><option value="pparasitica_eg_gene">Phytophthora parasitica genes (Phyt_para_P1569_V1)</option><option value="pramorum_eg_gene">Phytophthora ramorum genes (ASM14973v1)</option><option value="psojae_eg_gene">Phytophthora sojae genes (P.sojae V3.0)</option><option value="ptetraurelia_eg_gene">Paramecium tetraurelia genes (ASM16542v1)</option><option value="ptricornutum_eg_gene">Phaeodactylum tricornutum genes (ASM15095v2)</option><option value="pultimum_eg_gene">Pythium ultimum genes (pug)</option><option value="pvexans_eg_gene">Pythium vexans genes (pve_scaffolds_v1)</option><option value="pvivax_eg_gene">Plasmodium vivax genes (ASM241v2)</option><option value="tbrucei_eg_gene">Trypanosoma brucei genes (TryBru_Apr2005_chr11)</option><option value="tgondii_eg_gene">Toxoplasma gondii ME49 genes (TGA4)</option><option value="tpseudonana_eg_gene">Thalassiosira pseudonana genes (ASM14940v2)</option><option value="tthermophila_eg_gene">Tetrahymena thermophila genes (JCVI-TTA1-2.2)</option></xml></macros>\n\\ No newline at end of file\n' |
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| diff -r b6089425744d -r 5bf47c3cc3b9 macros_no_duplicates.xml --- a/macros_no_duplicates.xml Wed Nov 13 10:08:45 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,2 +0,0 @@\n-<?xml version=\'1.0\' encoding=\'utf-8\'?>\n-<macros><xml name="biomart"><option value="aastaci_eg_gene">Aphanomyces astaci genes (GCA000520075v1)</option><option value="aclavatus_eg_gene">Aspergillus clavatus NRRL 1 genes (ASM271v1)</option><option value="aflavus_eg_gene">Aspergillus flavus NRRL3357 genes (JCVI-afl1-v2.0)</option><option value="afumigatus_eg_gene">Aspergillus fumigatus Af293 genes (ASM265v1)</option><option value="afumigatusa1163_eg_gene">Aspergillus fumigatus A1163 genes (ASM15014v1)</option><option value="agossypii_eg_gene">Ashbya gossypii genes (ASM9102v1)</option><option value="ainvadans_eg_gene">Aphanomyces invadans genes (GCA000520115v1)</option><option value="anidulans_eg_gene">Aspergillus nidulans genes (ASM1142v1)</option><option value="aniger_eg_gene">Aspergillus niger genes (ASM285v2)</option><option value="aoryzae_eg_gene">Aspergillus oryzae RIB40 genes (ASM18445v3)</option><option value="aterreus_eg_gene">Aspergillus terreus NIH2624 genes (ASM14961v1)</option><option value="bbassiana_eg_gene">Beauveria bassiana genes (ASM168263v1)</option><option value="bcinerea_eg_gene">Botrytis cinerea B05.10 genes (ASM83294v1)</option><option value="bgraminis_eg_gene">Blumeria graminis genes (EF2)</option><option value="calbicans_eg_gene">Candida albicans genes (GCA000182965v3)</option><option value="cauris_eg_gene">Candida auris genes (GCA002759435v2)</option><option value="cduobushaemulonis_eg_gene">Candida duobushaemulonis genes (GCA002926085v1)</option><option value="cglabrata_eg_gene">Candida glabrata genes (GCA000002545v2)</option><option value="cgloeosporioides_eg_gene">Colletotrichum gloeosporioides genes (Colletotrichum gloeosporioides Nara gc-5)</option><option value="cgraminicola_eg_gene">Colletotrichum graminicola genes (C_graminicola_M1_001_V1)</option><option value="chaemuloni_eg_gene">[Candida] haemuloni genes (GCA002926055v1)</option><option value="chigginsianum_eg_gene">Colletotrichum higginsianum genes (ASM31379v2)</option><option value="cneoformans_eg_gene">Cryptococcus neoformans var. neoformans JEC21 genes (ASM9104v1)</option><option value="corbiculare_eg_gene">Colletotrichum orbiculare genes (Corbiculare240422v01)</option><option value="cparapsilosis_eg_gene">Candida parapsilosis genes (GCA000182765v2)</option><option value="cpseudohaemulonis_eg_gene">[Candida] pseudohaemulonii genes (GCA003013735v1)</option><option value="ctropicalis_eg_gene">Candida tropicalis genes (GCA000006335v3)</option><option value="dseptosporum_eg_gene">Dothistroma septosporum genes (Dothistroma septosporum NZE10 v1.0)</option><option value="fculmorum_eg_gene">Fusarium culmorum UK99 genes (EF 1)</option><option value="ffujikuroi_eg_gene">Fusarium fujikuroi genes (EF 1)</option><option value="fgraminearum_eg_gene">Fusarium graminearum str. PH-1 genes (RR1)</option><option value="foxysporum_eg_gene">Fusarium oxysporum genes (FO2)</option><option value="fpseudograminearum_eg_gene">Fusarium pseudograminearum genes (FP7)</option><option value="fsolani_eg_gene">Fusarium solani genes (v2.0)</option><option value="fverticillioides_eg_gene">Fusarium verticillioides genes (ASM14955v1)</option><option value="ggraminis_eg_gene">Gaeumannomyces tritici R3-111a-1 genes (Gae_graminis_V2)</option><option value="gultimum_eg_gene">Globisporangium ultimum genes (GCA000143045v1)</option><option value="hcapsulatum_eg_gene">Histoplasma capsulatum genes (GCA000170615v1)</option><option value="kpastoris_eg_gene">Komagataella pastoris genes (ASM2700v1)</option><option value="lmaculans_eg_gene">Leptosphaeria maculans genes (ASM23037v1)</option><option value="mlaricipopulina_eg_gene">Melampsora larici-populina genes (v1.0)</option><option value="moryzae_eg_gene">Magnaporthe oryzae genes (MG8)</option><option value="mpoae_eg_gene">Magnaporthe poae genes (Mag_poae_ATCC_64411_V1)</option><option value="mviolaceum_eg_gene">Microbotryum violaceum genes (M_violaceum_V1)</option><option value="ncrassa_eg_gene">Neurospora crassa genes '..b'ey_eg_gene">Triticum aestivum Stanley genes (PGSBv2.2_Stanley)</option><option value="taweebil_eg_gene">Triticum aestivum Weebill genes (EI_WeebilV1)</option><option value="tcacao_eg_gene">Theobroma cacao Matina 1-6 genes (Theobroma_cacao_20110822)</option><option value="tccriollo_eg_gene">Theobroma cacao Belizian Criollo B97-61/B2 genes (Criollo_cocoa_genome_V2)</option><option value="tdicoccoides_eg_gene">Triticum dicoccoides genes (WEWSeq v.1.0)</option><option value="tpratense_eg_gene">Trifolium pratense genes (Trpr)</option><option value="tspelta_eg_gene">Triticum spelta genes (PGSBv2.0_Spelta)</option><option value="tturgidum_eg_gene">Triticum turgidum genes (svevo)</option><option value="turartu_eg_gene">Triticum urartu genes (Tu2.0)</option><option value="vangularis_eg_gene">Vigna angularis genes (Vigan1.1)</option><option value="vradiata_eg_gene">Vigna radiata genes (Vradiata_ver6)</option><option value="vunguiculata_eg_gene">Vigna unguiculata genes (ASM411807v1)</option><option value="vvinifera_eg_gene">Vitis vinifera genes (PN40024.v4)</option><option value="zmays_eg_gene">Zea mays genes (Zm-B73-REFERENCE-NAM-5.0)</option><option value="alaibachii_eg_gene">Albugo laibachii genes (ENA 1)</option><option value="bnatans_eg_gene">Bigelowiella natans genes (Bigna1)</option><option value="ddiscoideum_eg_gene">Dictyostelium discoideum genes (dicty_2.7)</option><option value="ehistolytica_eg_gene">Entamoeba histolytica genes (JCVI-ESG2-1.0)</option><option value="ehuxleyi_eg_gene">Emiliania huxleyi genes (Emiliana huxleyi CCMP1516 main genome assembly v1.0)</option><option value="glamblia_eg_gene">Giardia lamblia genes (GL2)</option><option value="gtheta_eg_gene">Guillardia theta CCMP2712 genes (Guith1)</option><option value="harabidopsidis_eg_gene">Hyaloperonospora arabidopsidis genes (HyaAraEmoy2_2.0)</option><option value="lmajor_eg_gene">Leishmania major genes (ASM272v2)</option><option value="paphanidermatum_eg_gene">Pythium aphanidermatum genes (pag1_scaffolds_v1)</option><option value="parrhenomanes_eg_gene">Pythium arrhenomanes genes (par_scaffolds_v1)</option><option value="pberghei_eg_gene">Plasmodium berghei genes (PBANKA01)</option><option value="pchabaudi_eg_gene">Plasmodium chabaudi genes (PCHAS01)</option><option value="pfalciparum_eg_gene">Plasmodium falciparum 3D7 genes (ASM276v2)</option><option value="pinfestans_eg_gene">Phytophthora infestans genes (ASM14294v1)</option><option value="pirregulare_eg_gene">Pythium irregulare genes (pir_scaffolds_v1)</option><option value="piwayamai_eg_gene">Pythium iwayamai genes (piw_scaffolds_v1)</option><option value="pkernoviae_eg_gene">Phytophthora kernoviae genes (PhyKer238/432v1)</option><option value="pknowlesi_eg_gene">Plasmodium knowlesi genes (ASM635v1)</option><option value="plateralis_eg_gene">Phytophthora lateralis genes (MPF4_v1.0)</option><option value="pmultistriata_eg_gene">Pseudo-nitzschia multistriata genes (ASM90066040v1)</option><option value="pparasitica_eg_gene">Phytophthora parasitica genes (Phyt_para_P1569_V1)</option><option value="pramorum_eg_gene">Phytophthora ramorum genes (ASM14973v1)</option><option value="psojae_eg_gene">Phytophthora sojae genes (P.sojae V3.0)</option><option value="ptetraurelia_eg_gene">Paramecium tetraurelia genes (ASM16542v1)</option><option value="ptricornutum_eg_gene">Phaeodactylum tricornutum genes (ASM15095v2)</option><option value="pultimum_eg_gene">Pythium ultimum genes (pug)</option><option value="pvexans_eg_gene">Pythium vexans genes (pve_scaffolds_v1)</option><option value="pvivax_eg_gene">Plasmodium vivax genes (ASM241v2)</option><option value="tbrucei_eg_gene">Trypanosoma brucei genes (TryBru_Apr2005_chr11)</option><option value="tgondii_eg_gene">Toxoplasma gondii ME49 genes (TGA4)</option><option value="tpseudonana_eg_gene">Thalassiosira pseudonana genes (ASM14940v2)</option><option value="tthermophila_eg_gene">Tetrahymena thermophila genes (JCVI-TTA1-2.2)</option></xml></macros>\n\\ No newline at end of file\n' |
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| diff -r b6089425744d -r 5bf47c3cc3b9 rgreat.xml --- a/rgreat.xml Wed Nov 13 10:08:45 2024 +0000 +++ b/rgreat.xml Wed Nov 13 15:17:44 2024 +0000 |
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| @@ -1,6 +1,6 @@ <tool id="rgreat" name="Genomic Regions Enrichment of Annotations Tool" version="0.1.0+galaxy0" profile="21.05"> <macros> - <import>macros_no_duplicates.xml</import> + <import>macros.xml</import> </macros> <requirements> <requirement type="package" version="4.3.0">r-base</requirement> |
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| diff -r b6089425744d -r 5bf47c3cc3b9 upload_data.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/upload_data.py Wed Nov 13 15:17:44 2024 +0000 |
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| @@ -0,0 +1,39 @@ +import os +import glob +from bioblend.galaxy import GalaxyInstance + +# Galaxy instance details +galaxy_url = "http://127.0.0.1:8080/" # Replace with your Galaxy URL +api_key = "2f9c202b5a9e4de7ba5198df98e8b1a2" # Replace with your actual API key + +# Initialize the Galaxy instance +gi = GalaxyInstance(url=galaxy_url, key=api_key) + +# Path to the file you want to upload +#file_path = "/mnt/jonas/methylator-galaxy/test_data/WGBS/GRCm38.p4.genome.fa" # Replace with the actual file path + +new_history = gi.histories.create_history(name="test 1 upload") +history_id = new_history['id'] +#history_id = 'ae83c66a72925a01' + +# Directory containing the fastq files +#fastq_dir = "/mnt/jonas/methylator-galaxy/planemo/dmrseq_tool/test-data" # Replace with the actual directory path +#files_upload = ("test-data/dmrseq_1208_1137.rdata", "test-data/dmrseq_output.rdata") +#files_upload = "test-data/sim_DMRs.rds" +#files_upload = mylist = [f for f in glob.glob("/mnt/jonas/methylator-galaxy/test_data/WGBS/Habibi2013_chr6_F3A/analysis/methXT/SR*")] +files_upload = "/Users/admin_urpp/Desktop/methylator-galaxy/galaxy/tools/my_tools/bismark2bedgraph/test_data/CpG_context.txt" + +# Function to upload a file +def upload_file(file_path): + try: + uploaded_file = gi.tools.upload_file(file_path, history_id=history_id) + print(f"Uploaded: {os.path.basename(file_path)} - Dataset ID: {uploaded_file['outputs'][0]['id']}") + except Exception as e: + print(f"Error uploading {os.path.basename(file_path)}: {str(e)}") + +#for file_path in files_upload: +# upload_file(file_path) + +upload_file(files_upload) + +print("Upload process completed.") \ No newline at end of file |