mgnify-amplicon-pipeline-v5-its/main
v0.1

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Classification and visualization of ITS regions.

SEEK ID: https://workflowhub.eu/workflows/1273?version=1

Inputs

ID Name Description Type
LSU and SSU BED LSU and SSU BED A BED file containing the LSU and SSU coordinates.
  • File[]
Processed sequences Processed sequences Processed sequences.
  • File[]

Steps

ID Name Description
2 Filter empty datasets __FILTER_EMPTY_DATASETS__
3 Extract element identifiers toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
4 Filter collection __FILTER_FROM_FILE__
5 bedtools MaskFastaBed toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_maskfastabed/2.31.1
6 MAPseq toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0
7 MAPseq toolshed.g2.bx.psu.edu/repos/iuc/mapseq/mapseq/2.1.1+galaxy0
8 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
9 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
10 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
11 Filter empty datasets __FILTER_EMPTY_DATASETS__
12 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
13 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
14 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
15 Filter empty datasets __FILTER_EMPTY_DATASETS__
16 Filter empty datasets __FILTER_EMPTY_DATASETS__
17 Filter empty datasets __FILTER_EMPTY_DATASETS__
18 Filter empty datasets __FILTER_EMPTY_DATASETS__
19 Map empty/not empty collection to boolean n/a
20 Filter empty datasets __FILTER_EMPTY_DATASETS__
21 Filter empty datasets __FILTER_EMPTY_DATASETS__
22 Filter empty datasets __FILTER_EMPTY_DATASETS__
23 Map empty/not empty collection to boolean n/a
24 Map empty/not empty collection to boolean n/a
25 Krona ITSoneDB toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
26 Map empty/not empty collection to boolean n/a
27 Krona ITS UNITE toolshed.g2.bx.psu.edu/repos/crs4/taxonomy_krona_chart/taxonomy_krona_chart/2.7.1+galaxy0
28 HDF5 ITSoneDB toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1
29 JSON ITSoneDB toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1
30 HDF5 ITS UNITE toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1
31 JSON ITS UNITE toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert/2.1.15+galaxy1

Outputs

ID Name Description Type
ITS FASTA files ITS FASTA files n/a
  • File
ITS taxonomic classifications using ITSoneDB ITS taxonomic classifications using ITSoneDB n/a
  • File
ITS OTU tables (ITSoneDB) ITS OTU tables (ITSoneDB) n/a
  • File
ITS taxonomic classifications using UNITE DB ITS taxonomic classifications using UNITE DB n/a
  • File
ITS OTU tables (UNITE DB) ITS OTU tables (UNITE DB) n/a
  • File
ITS taxonomic abundance pie charts (ITSoneDB) ITS taxonomic abundance pie charts (ITSoneDB) n/a
  • File
ITS taxonomic abundance pie charts (UNITE DB) ITS taxonomic abundance pie charts (UNITE DB) n/a
  • File
ITS OTU tables in HDF5 format (ITSoneDB) ITS OTU tables in HDF5 format (ITSoneDB) n/a
  • File
ITS OTU tables in JSON format (ITSoneDB) ITS OTU tables in JSON format (ITSoneDB) n/a
  • File
ITS OTU tables in HDF5 format (UNITE DB) ITS OTU tables in HDF5 format (UNITE DB) n/a
  • File
ITS OTU tables in JSON format (UNITE DB) ITS OTU tables in JSON format (UNITE DB) n/a
  • File

Version History

v0.1 (earliest) Created 4th Feb 2025 at 03:02 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 71fd211
help Creators and Submitter
Creators
Additional credit

EMBL's European Bioinformatics Institute

Submitter
Tools
BEDTools
MAPseq
taxonomy_krona_chart
biomformat
License
Apache License 2.0
Activity

Views: 11   Downloads: 3   Runs: 0

Created: 4th Feb 2025 at 03:02

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