extend_align.yaml

!mobyle/program
name: extend_align
title: concatenate several alignments from several files
description: This tool concatenates multiple MSAs.
authors: "N\xE9ron, B."
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        comment: "<html:div xmlns:html=\"http://www.w3.org/1999/xhtml\"><html:ol><html:li>by\
            \ sequence order: in this case the ids of sequences could be different.\n\
            \             and the id of each sequence in the resulting alignment is\
            \ the concatenation of the respective sequence id \n             (All\
            \ Alignments MUST have the same number of sequences)</html:li><html:li>by\
            \ sequence id: in this case the extension is made based on the sequence\
            \ ids.</html:li></html:ol></html:div>"
        prompt: method to extend the alignment
        format: ( "" , " --id ")[value is not None and value != vdef]
        argpos: 5
        name: extend_method
        command: false
        type: !mobyle/stringtype
            default: 'null'
            options:
            - {label: by order, value: 'null'}
            - {label: by id, value: id}
    - !mobyle/inputprogramparameter {prompt: alignment, format: '" -i " + value +
            " fasta"', simple: true, argpos: 10, mandatory: true, name: fasta_align,
        command: false}
    - !mobyle/inputprogramparameter
        prompt: sequence linker
        format: ("", " -l " + str( value ) )[value is not None]
        argpos: 100
        name: linker
        command: false
        type: !mobyle/stringtype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: concatenated alignment
        filenames: '"extend_align.out"'
        name: concatenated_alignment
        output_type: stdout
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:0863']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"extend_align.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
comment: "<html:div xmlns:html=\"http://www.w3.org/1999/xhtml\"><html:p>for instance</html:p>fisrt\
    \ alignment<html:pre>&gt;seq1\n            aaaaggg\n            &gt;seq2\n   \
    \         aaaa--g\n            &gt;seq3\n            aa--ggg</html:pre>second\
    \ alignment<html:pre>&gt;seq1\n            ccccttt\n            &gt;seq2\n   \
    \         cccc--t\n            &gt;seq3\n            cc--ttt</html:pre>the resulting\
    \ alignment if the linker is \"---\" will be:<html:pre>&gt;seq1\n            aaaaggg---ccccttt\n\
    \            &gt;seq2\n            aaaa--g---cccc--t\n            &gt;seq3\n \
    \           aa--ggg---cc--ttt</html:pre>two methods can be used to extend the\
    \ aligenmt:<html:ol><html:li>by sequence order: in this case the ids of sequences\
    \ could be different.\n             and the id of each sequence in the resulting\
    \ alignment is the concatenation of the respective sequence id \n            \
    \ (All Alignments MUST have the same number of sequences)</html:li><html:li>by\
    \ sequence id: in this case the extension is made based on the sequence ids.</html:li></html:ol></html:div>"
operations: ['EDAM_operation:2122']
topics: ['EDAM_topic:0220']
command: extend_align
env: {}