| input type | input format | operation | output type | output format | bash | comment |
|---|---|---|---|---|---|---|
| Protein report (http://edamontology.org/data_0896) | protXML (http://edamontology.org/format_3747) | Conversion (http://edamontology.org/operation_3434) | ID list (http://edamontology.org/data_2872) | TSV (http://edamontology.org/format_3475) | #!/bin/bash xmllint --xpath "//*[local-name()='protein']/@protein_name" $1 | cut -d '|' -f2 > $2 |
assumes UniProt style FASTA was used |