fastaRename_1.0.yaml

!mobyle/program
name: fastaRename
version: '1.0'
title: fasta header shortener
description: helps out with the 10-character limit of the PHYLIP-PHYML formats
authors: "Bertrand N\xE9ron"
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter
        prompt: Input sequence file
        format: '" " + str(value)'
        simple: true
        argpos: 1
        mandatory: true
        name: input
        command: false
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:0863']
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        comment: type any kind of text
        prompt: Output file with renamed headers
        filenames: '"*.rename.fasta"'
        name: output_fasta
        type: !mobyle/formattedtype
            format_terms: ['EDAM_format:2200']
            data_terms: ['EDAM_data:0863']
    - !mobyle/outputprogramparameter {prompt: Output file header map, filenames: '"*.map"',
        name: output_map}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"fastaRename.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"fastaRename.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
comment: "<html:div xmlns:html=\"http://www.w3.org/1999/xhtml\">Due to an incompatibility\
    \ between the PHYLIP format and phyml and morePhyml named rules, \n          \
    \  the using of long identifier in phyml or morePhyml failed. We proposed the\
    \ following workaround:<html:ol><html:li>use fastaRename to generate an alignment\
    \ with short ID and a file of ID mapping</html:li><html:li>perform your analysis\
    \ with the alignment with short id</html:li><html:li>replace the short IDs in\
    \ your tree (in NEWICK format) with nw_rename and the file of IDs mapping generated\
    \ at the step 1.</html:li></html:ol></html:div>"
operations: ['EDAM_operation:2121']
topics: ['EDAM_topic:0220']
command: fastaRename
env: {}