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Available commands showing more than commands declared #65

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Luis-WP-Arge opened this issue Sep 28, 2024 · 0 comments
Open

Available commands showing more than commands declared #65

Luis-WP-Arge opened this issue Sep 28, 2024 · 0 comments

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@Luis-WP-Arge
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Luis-WP-Arge commented Sep 28, 2024

Hi

I'm trying to use koi but I'm facing a problem with the section Available commands.
Below is my script and command output:

#!/bin/bash

#set -x #For development purpose only
set -o pipefail

source koi/koi

koiname=gwgfscan
koidescription="GWGFScan: A pipeline to perform genome wide identification of gene families of interest"

function greet {
    __addarg "-h" "--help"       "help"            "optional" ""      "Just a little help on how to run this tool"
    __addarg ""   "name"         "positionalvalue" "required" ""      "The name of someone you like"
    __addarg "-s" "--salutation" "storevalue"      "optional" "Hello" "The greeting to use"
    __addarg "-e" "--exclaim"    "flag"            "optional" ""      "If include, greeting will be exclaimed"
    __parseargs "$@"

    local exclaim_text=
    if [[ $exclaim -eq 1 ]] ; then
       exclaim_text='!'
    fi

    echo "${salutation}, ${name}${exclaim_text}"
}


__koirun "$@"

Output:

GWGFScan: A pipeline to perform genome wide identification of gene families of interest

Usage:
  gwgfscan COMMAND [args]

Available commands:
  declare
  -fx
  _module_raw
  greet
  help
  list
  declare
  -fx
  ml
  declare
  -fx
  module

Hints:
  gwgfscan help --verbose    Show complete command documentation
  gwgfscan COMMAND --help    Show individual command documentation

Is there a way to remove these other command options?

Thanks,
Willian

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