<commit_before><tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1">
  <description>from taxonomic profile</description>
  <requirements>
    <requirement type="package" version="2.6.1">krona</requirement>
  </requirements>
  <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
  <command detect_errors="exit_code"><![CDATA[
    #import re

    #if $type_of_data.input[0].is_of_type('taxonomy'):
        ktImportGalaxy
        -d '${type_of_data.max_rank}'
        -n '${root_name}'
        -o '${output}'
        ${combine_inputs}
        #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
            '${input_dataset},${input_count}'
        #end for
    #else:
        ktImportText
        -n '${root_name}'
        -o '${output}'
        ${combine_inputs}
        #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
             #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
            '${input_dataset},${identifier}'
        #end for
    #end if
    &&
    if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi
  ]]></command>
  <inputs>
    <conditional name="type_of_data"><commit_msg>remove enumeration<commit_after><tool id="taxonomy_krona_chart" name="Krona pie chart" version="2.6.1">
  <description>from taxonomic profile</description>
  <requirements>
    <requirement type="package" version="2.6.1">krona</requirement>
  </requirements>
  <version_command>ktImportText | sed -n 's/.*\(KronaTools [[:digit:].]\{1,\}\).*/\1/p'</version_command>
  <command detect_errors="exit_code"><![CDATA[
    #import re

    #if $type_of_data.input[0].is_of_type('taxonomy'):
        ktImportGalaxy
        -d '${type_of_data.max_rank}'
        -n '${root_name}'
        -o '${output}'
        ${combine_inputs}
        #for $input_count, $input_dataset in enumerate( $type_of_data.input ):
            '${input_dataset},${input_count}'
        #end for
    #else:
        ktImportText
        -n '${root_name}'
        -o '${output}'
        ${combine_inputs}
        #for $input_dataset in $type_of_data.input:
             #set $identifier=re.sub('[^\w\-\s]', '_', str($input_dataset.element_identifier))
            '${input_dataset},${identifier}'
        #end for
    #end if
    &&
    if [ -d '${output}.files' ] ; then mkdir '${output.extra_files_path}' && mv '${output}.files' '${output.extra_files_path}' ; fi
  ]]></command>
  <inputs>
    <conditional name="type_of_data">
{'fraction_non_alphanumeric': 0.18265541059094398, 'fraction_numerical': 0.006907137375287797, 'mean_word_length': 3.131537242472266, 'pattern_counts': {'":': 0, '<': 31, '<?xml version=': 0, '>': 31, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3828576', 'n_tokens_mistral': 920, 'n_tokens_neox': 893, 'n_words': 152}