cosa.yaml

!mobyle/program
name: cosa
title: cosa
description: Clustal ouput structural analysis
authors: T. Rose
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        prompt: Alignment
        format: '" "+str(value)'
        simple: true
        argpos: 1
        mandatory: true
        name: alig
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:1982']
            data_terms: ['EDAM_data:1384']
    - !mobyle/inputprogramparameter
        prompt: Position in the sequence multialignment of the structure used as reference
        format: '" " + str( value )'
        simple: true
        argpos: 2
        mandatory: true
        name: struct_pos
        command: false
        type: !mobyle/integertype {}
    - !mobyle/inputprogramparameter {prompt: PDB entry, format: '" " + str( value
            )', simple: true, argpos: 3, mandatory: true, name: pdbin, command: false}
    - !mobyle/inputprogramparameter
        prompt: Name of the output PDB file
        format: ("", " " + str( value ) )[ value is not None ]
        argpos: 4
        name: pdbout
        command: false
        type: !mobyle/stringtype {default: tmp_clustal.pdb}
    - !mobyle/inputprogramparameter
        prompt: Name of the output result file
        format: ("" , " " + str( value ) )[ value is not None ]
        argpos: 5
        name: txtout
        command: false
        type: !mobyle/stringtype {default: tmp_stats.txt}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter {comment: "PDB file format of the structure used\
            \ as reference with \n        the residue occurrence in place of B-factor",
        prompt: PDB with the residue occurrence, filenames: pdbout, name: default_pdbout}
    - !mobyle/outputprogramparameter {comment: Vertical sequence alignment and statistics,
        prompt: Alignment and statistics, filenames: txtout, name: default_txtout}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"cosa.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"cosa.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
comment: This program gives simple statistics about residue conservation from clustal
    output files.There is the possibility to redirect the residue frequency at every
    position of the proteinsequence in the PDB file corresponding to one of the identified
    sequences of the multiple alignment.This frequency or conservation index is put
    in place of B-factors and allows spectral coloring according tothe index value
    in most of pdb structure viewers.
operations: ['EDAM_operation:2506', 'EDAM_operation:0448']
topics: ['EDAM_topic:0182']
command: cosa
env: {}