compute_principal__0.0.1.yaml

!mobyle/program
name: compute_principal_
version: 0.0.1
title: compute_principal_
description: Compute principal components given a .hud file.
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter {prompt: contents of a .hud file, format: '" --hud="
            + str(value)', simple: true, argpos: 1, mandatory: true, name: hud, command: false}
    - !mobyle/inputprogramparagraph
        prompt: input options
        name: input_options
        children:
        - !mobyle/inputprogramparameter
            prompt: the data source is really diploid and biallelic
            format: '" --diploid_and_biallelic=" + ("Y" if value else "N")'
            simple: true
            argpos: 2
            mandatory: true
            name: diploid_and_biallelic
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparameter
        prompt: find this many principal components
        format: '" --npcs=" + str(value)'
        simple: true
        argpos: 3
        mandatory: true
        name: npcs
        command: false
        type: !mobyle/integertype {default: 3}
    - !mobyle/inputprogramparagraph
        prompt: output options
        name: output_options
        children:
        - !mobyle/inputprogramparameter
            prompt: add row indices for R table compatibility
            format: '" --add_indices=" + ("Y" if value else "N")'
            simple: true
            argpos: 4
            mandatory: true
            name: add_indices
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: force first-column elements to be IC-prefixed
            format: '" --clean_isolates=" + ("Y" if value else "N")'
            simple: true
            argpos: 5
            mandatory: true
            name: clean_isolates
            command: false
            type: !mobyle/booleantype {default: false}
    - !mobyle/inputprogramparameter
        prompt: write to file for mobyle
        format: '" --write_to_file_for_mobyle"'
        argpos: 6
        name: write_to_file_for_mobyle
        command: false
        hidden: true
        type: !mobyle/booleantype {}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter {prompt: compute_principal__out, filenames: '"out.table"',
        name: compute_principal__out}
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"compute_principal_.out"'
        name: stdout
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"compute_principal_.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
command: runbsub -n 1 -W 720 -q dean -o result.out -e result.err __bsubArgsEnd__ /usr/local/apps/python-2.6.5/bin/python
    /home/mobyle/pca/auto.py 20100608a
env: {}