blast2seqid_1.0.yaml

!mobyle/program
name: blast2seqid
version: '1.0'
title: blast2seqid
description: Extract sequence Ids from blast hits (in USA format)
authors: "Bertrand N\xE9ron"
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        comment: A blast output in pairwise format ( option -m 0 default ).
        prompt: BLAST text report
        format: '" "+str(value)'
        simple: true
        argpos: 40
        mandatory: true
        name: infile
        command: false
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:0857']
    - !mobyle/inputprogramparagraph
        prompt: Output options
        name: output
        children:
        - !mobyle/inputprogramparameter
            prompt: ignore the hits until the hit n (integer)
            format: ( "" , " --from " + str(value) )[value is not None]
            argpos: 10
            name: From
            command: false
            type: !mobyle/integertype {}
        - !mobyle/inputprogramparameter
            prompt: ignore the hits after the hit n (integer)
            format: ( "" , " --to " + str(value) )[value is not None]
            argpos: 20
            name: To
            command: false
            type: !mobyle/integertype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter {prompt: hits identifier, filenames: '"blast2seqid.out"',
        name: id_list, output_type: stdout}
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"blast2seqid.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
comment: "Extract the Identifier and Data Bank of the hits\n                    from\
    \ the summary of a blast report ( in text format -m 0-6 ) \n                 \
    \   The result is in USA list format."
homepage_links: ['https://projets.pasteur.fr/projects/show/blast2usa']
command: blast2usa
env: {}
source_links: ['https://projets.pasteur.fr/projects/list_files/blast2usa']