Table 1: Names, types, descriptions and locations of primary data and additional scripts referenced in this article

From: Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes

File Name Description Type Location URL Data Record Accession
Dockerfile Source code for building the container image Text GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
galaxy/mtbls520_workflow.ga Galaxy workflow XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
galaxy/mtbls520_workflow.jpg Screenshot of the workflow running in Galaxy JPG GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
korseby/mtbls520 Container image Container Dockerhub https://hub.docker.com/r/korseby/mtbls520/ korseby/mtbls520
m_bryos_metabolite_*_negative_mode.maf Peak table matrix of bryophyte samples (negative mode) Tabular Separated MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520
m_bryos_metabolite_*_positive_mode.maf Peak table matrix of bryophyte samples (positive mode) Tabular Separated MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520
m_bryos_quality_*_negative_mode.maf Peak table matrix of QC samples (negative mode) Tabular Separated MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520
m_bryos_quality_*_positive_mode.maf Peak table matrix of QC samples (positivemode) Tabular Separated MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520
m_characteristics.csv Ecological characteristics of the bryophyte species compiled from literature Comma Separated MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520, doi:<NEW_PHYTOL>
m_moss_phylo.tre Phylogenetic distances of bryophyte species Tree MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520
mtbls520_01_mtbls_download.sh Script: Download the whole study from MetaboLights Shell script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_01_mtbls_download.xml Galaxy module: Download the whole study from MetaboLights XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_02_extract.sh Script: Extract files from a downloaded MetaboLights archive Shell script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_02_extract.xml Galaxy module: Extract files from the downloaded MetaboLights archive XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_03_qc_perform.r Script: Perform Quality Control R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_03_qc_preparations.sh Script: Make preparations for the QC Shell script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_03_quality_control.xml Galaxy module: Process the quality control pipeline XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_04_preparations.r Script: Preparations and settings for files and the R environment R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_04_preparations.sh Script: Import peak table matrix Shell script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_04_preparations.xml Galaxy module: Preparations and settings for files and the R environment XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_05a_import_maf.r Script: Generating matrix for diversity calculations R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_05a_import_maf.xml Galaxy module: Import peak table matrix XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_06_import_traits.r Script: Import ecological characteristics R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_06_import_traits.xml Galaxy module: Import ecological characteristics XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_07_species_diversity.r Script: Create species unique features plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_07_species_diversity.xml Galaxy module: Generating matrix for diversity calculations XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_08a_species_shannon.r Script: Create species Shannon diversity plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_08a_species_shannon.xml Galaxy module: Create species Shannon diversity plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_08b_species_unique.r Script: Create species unique features plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_08b_species_unique.xml Galaxy module: Create species unique features plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_08c_species_variability.r Script: Create species variability plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_08c_species_variability.xml Galaxy module: Create species variability plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_08d_concentration.xml Galaxy module: Create species metabolite concentration plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_08d_species_concentration.r Script: Create species concentration plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_09_species_venn.r Script: Create Venn diagram plots R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_09_species_venn.xml Galaxy module: Create species Venn plots XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_10_species_varpart.r Script: Create variation partitioning plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_10_species_varpart.xml Galaxy module: Create variation partitioning plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_12_species_marchantia.r Script: Create annotation of Marchantia polymorpha profile R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_12_species_marchantia.xml Galaxy module: Create annotation of Marchantia polymorpha profile plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_16_ecology_rda.r Script: Create ecology dbRDA plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_16_ecology_rda.xml Galaxy module: Create ecology dbRDA plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_18_phylogeny.r Script: Create phylogeny and chemotaxonomy plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_18_phylogeny.xml Galaxy module: Create phylogeny and chemotaxonomy plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_19a_seasons_shannon.r Script: Create seasons Shannon diversity plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_19a_seasons_shannon.xml Galaxy module: Create seasons Shannon diversity plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_19b_seasons_unique.r Script: Create seasons unique features plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_19b_seasons_unique.xml Galaxy module: Create seasons unique features plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_19c_seasons_variability.r Script: Create seasons variability plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_19c_seasons_variability.xml Galaxy module: Create seasons variability plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_19d_seasons_concentration.r Script: Create seasons concentration plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_19d_seasons_concentration.xml Galaxy module: Create seasons metabolite concentration plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_23_seasons_rda.r Script: Create seasons dbRDA plot R script GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
mtbls520_23_seasons_rda.xml Galaxy module: Create seasons RDA plot XML GitHub https://github.com/korseby/container-mtbls520 korseby/container-mtbls520
neg_[01-27]_*.mzML Metabolite profiles of the bryophyte species measured in negative mode Raw MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520
neg_MM8_*.mzML Quality control profiles measured in negative mode Raw MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520
pos_[01-27]_*.mzML Metabolite profiles of the bryophyte species measured in positive mode Raw MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520
pos_MM8_*.mzML Quality control profiles measured in positive mode Raw MetaboLights 520 (Data Citation 1: MetaboLights MTBLS520) https://www.ebi.ac.uk/metabolights/MTBLS520 MTBLS520