comparison regex_tabular.xml @ 2:538933d9fccc draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/regex_find_replace commit 8871a847daed1f996c0a2069c3e876685bf8d220"

1:209b7c5ee9d7

<tool id="regexColumn1" name="Column Regex Find And Replace" version="1.0.0">
  <description></description>
  <command interpreter="python">regex.py --input '$input' --output '$out_file1' --column $field --input_display_name '$input.display_name'
    #for $check in $checks:
    --pattern='$check.pattern' --replacement='$check.replacement'
    #end for
  </command>
  <inputs>
    <param format="tabular" name="input" type="data" label="Select cells from"/>
    <param name="field" label="using column" type="data_column" data_ref="input" />
    <repeat name="checks" title="Check">
      <param name="pattern" size="40" type="text" value="chr([0-9A-Za-z])+" label="Find Regex" help="here you can enter text or regular expression (for syntax check lower part of this frame)">
        <sanitizer>
          <valid>
            <add preset="string.printable"/>
            <remove value="&#92;" />
            <remove value="&apos;" />

            <add source="&#92;" target="__backslash__" />
            <add source="&apos;" target="__sq__"/>
          </mapping>
        </sanitizer>
      </param>
      <param name="replacement" size="40" type="text" value="newchr\1" label="Replacement">
        <sanitizer>
          <valid>
            <add preset="string.printable"/>
            <remove value="&#92;" />
            <remove value="&apos;" />

2:538933d9fccc

<tool id="regexColumn1" name="Column Regex Find And Replace" version="1.0.1">
  <description></description>
  <requirements>
    <requirement type="package" version="3.7">python</requirement>
  </requirements>
  <command>
    python '$__tool_requirements__/regex.py'
      --input '$input'
      --output '$out_file1'
      --column $field
      --input_display_name '$input.display_name'
      #for $check in $checks:
        --pattern='$check.pattern' --replacement='$check.replacement'
      #end for
  </command>
  <inputs>
    <param format="tabular" name="input" type="data" label="Select cells from"/>
    <param name="field" label="using column" type="data_column" data_ref="input" />
    <repeat name="checks" title="Check">
      <param name="pattern" type="text" value="chr([0-9A-Za-z])+" label="Find Regex" help="here you can enter text or regular expression (for syntax check lower part of this frame)">
        <sanitizer>
          <valid>
            <add preset="string.printable"/>
            <remove value="&#92;" />
            <remove value="&apos;" />

            <add source="&#92;" target="__backslash__" />
            <add source="&apos;" target="__sq__"/>
          </mapping>
        </sanitizer>
      </param>
      <param name="replacement" type="text" value="newchr\1" label="Replacement">
        <sanitizer>
          <valid>
            <add preset="string.printable"/>
            <remove value="&#92;" />
            <remove value="&apos;" />