tripal/tripal_galaxy

Expected one space after the comma, 0 found

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  $fasta_aliases = ['fasta','fa','fna','faa','gz'];

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Expected one space after the comma, 0 found

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          if (!in_array($alias_to_add,$input['extensions'])) {

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Inline comments must end in full-stops, exclamation marks, colons, question marks, or closing parentheses

Invalid

      // phpcs:disable Squiz.PHP.NonExecutableCode.Unreachable

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Line indented incorrectly; expected 4 spaces, found 6

Invalid

      // phpcs:enable Squiz.ControlStructures.SwitchDeclaration.SpacingAfterBreak

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Inline comments must start with a capital letter

Open

  // gff aliases

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Inline comments must start with a capital letter

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  // combined for loopiness

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Inline comments must end in full-stops, exclamation marks, colons, question marks, or closing parentheses

Open

  // combined for loopiness

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Line exceeds 80 characters; contains 82 characters

Invalid

      // phpcs:disable Squiz.ControlStructures.SwitchDeclaration.SpacingAfterBreak

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Expected one space after the comma, 0 found

Open

  $fastq_aliases = ['fastq','fq','fastqsanger','fastqillumina','fastqsolexa','gz'];

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There must be no blank line following an inline comment

Invalid

      // phpcs:enable Squiz.ControlStructures.SwitchDeclaration.SpacingAfterBreak

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Inline comments must end in full-stops, exclamation marks, colons, question marks, or closing parentheses

Open

  // Loop through all arrays of aliases first, check if we're dealing with any types that require aliases

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Type hint "scalar" missing for $value

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function _tripal_galaxy_invoke_webform_build_values(array &$values, string $input_full_name, $value) {

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Line indented incorrectly; expected 4 spaces, found 6

Invalid

      // phpcs:enable Squiz.PHP.NonExecutableCode.Unreachable

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Expected one space after the comma, 0 found

Open

  $fasta_aliases = ['fasta','fa','fna','faa','gz'];

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Inline comments must end in full-stops, exclamation marks, colons, question marks, or closing parentheses

Open

  // gff aliases

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Expected one space after the comma, 0 found

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  $gff_aliases = ['gff','gff3', 'gz'];

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Line exceeds 80 characters; contains 88 characters

Open

        // Loop through the rest of the aliases and add them if they don't already exist

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Case breaking statements must be followed by a single blank line

Invalid

      return;

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Expected one space after the comma, 0 found

Open

  $fastq_aliases = ['fastq','fq','fastqsanger','fastqillumina','fastqsolexa','gz'];

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Expected one space after the comma, 0 found

Open

  $alias_lists = array($fasta_aliases,$fastq_aliases,$gff_aliases);

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Expected one space after the comma, 0 found

Open

  $fastq_aliases = ['fastq','fq','fastqsanger','fastqillumina','fastqsolexa','gz'];

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Expected one space after the comma, 0 found

Open

  $fastq_aliases = ['fastq','fq','fastqsanger','fastqillumina','fastqsolexa','gz'];

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Expected one space after the comma, 0 found

Open

  $fastq_aliases = ['fastq','fq','fastqsanger','fastqillumina','fastqsolexa','gz'];

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Concat operator must be surrounded by a single space

Open

            echo "Added ". $alias_to_add . " to a list\n<br />";

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If the line declaring an array spans longer than 80 characters, each element should be broken into its own line

Open

  $fastq_aliases = ['fastq','fq','fastqsanger','fastqillumina','fastqsolexa','gz'];

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Inline comments must end in full-stops, exclamation marks, colons, question marks, or closing parentheses

Open

        // Loop through the rest of the aliases and add them if they don't already exist

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There must be no blank line following an inline comment

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  // the aliases is found, which may be a naive approach.

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Inline comments must start with a capital letter

Open

  // fasta aliases (includes compressed versions just in case)

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Inline comments must start with a capital letter

Open

  // fastq aliases (includes compressed versions just in case)

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Inline comments must end in full-stops, exclamation marks, colons, question marks, or closing parentheses

Invalid

      // phpcs:enable Squiz.ControlStructures.SwitchDeclaration.SpacingAfterBreak

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Expected one space after the comma, 0 found

Open

  $fasta_aliases = ['fasta','fa','fna','faa','gz'];

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Expected one space after the comma, 0 found

Open

  $fasta_aliases = ['fasta','fa','fna','faa','gz'];

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Missing parameter type

Open

 * @param $webform

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Line exceeds 80 characters; contains 105 characters

Open

  // Loop through all arrays of aliases first, check if we're dealing with any types that require aliases

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Inline comments must end in full-stops, exclamation marks, colons, question marks, or closing parentheses

Open

        // No need to keep checking for aliases in this list, proceed

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Code after RETURN statement cannot be executed

Invalid

    break;

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Line exceeds 80 characters; contains 81 characters

Invalid

      // phpcs:enable Squiz.ControlStructures.SwitchDeclaration.SpacingAfterBreak

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Expected one space after the comma, 0 found

Open

  $alias_lists = array($fasta_aliases,$fastq_aliases,$gff_aliases);

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Whitespace found at end of line

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Whitespace found at end of line

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  // ($filetype_aliases). The entire array is added if even one of 

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Whitespace found at end of line

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  // files that require aliases is so small (fa, fq). For now, if 

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Whitespace found at end of line

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  foreach ($alias_lists as $alias_list) { 

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Whitespace found at end of line

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  // additional aliases are needed, add a new array as below 

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Whitespace found at end of line

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