<commit_before><?xml version="1.0"?>
<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="35-2">
    <description>BLAST-like sequence alignment tool</description>
    <requirements>
      <requirement type="package" version="35">blat</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if str($reference_source.reference_source_selector) == "history":
            ## blat depends on file extension
            #if $reference_source.database.is_of_type("fasta"):
                #set $reference_fasta_filename = "localref.fa"
            #elif $reference_source.database.is_of_type("twobit"):
                #set $reference_fasta_filename = "localref.2bit"
            #else
                #set $reference_fasta_filename = "localref"
            #end if

            ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
      #else:
            #set $reference_fasta_filename = str($reference_source.database.fields.path)
      #end if

      blat

            -q=$query_type
            -t=$database_type

            #if $oneOff
              -oneOff=1
            #end if

            #if str($minScore)
              '-minScore=${minScore}'
            #end if

            '-maxGap=${maxGap}'

            #if str($repMatch)
              '-repMatch=${repMatch}'
            #end if

            #if $mask_type.mask == "file.out":
                  -mask='${mask_type.mask_file}'
            #else:
                  -mask=$mask_type.mask
            #end if

            #if str($dots)
              '-dots=${dots}'
            #end if

            ${trimT}
            ${noTrimA}
            ${trimHardA}
            ${fastMap}
            ${fine}

            #if str($maxIntron)
             '-maxIntron=${maxIntron}'
            #end if

            ${extendThroughN}

            '$reference_fasta_filename'
            '${query}'

            -out=${out}

            '${output}'
]]></command>
      <inputs>
            <conditional name="reference_source"><commit_msg>Remove quotes for integer<commit_after><?xml version="1.0"?>
<tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="35-2">
    <description>BLAST-like sequence alignment tool</description>
    <requirements>
      <requirement type="package" version="35">blat</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if str($reference_source.reference_source_selector) == "history":
            ## blat depends on file extension
            #if $reference_source.database.is_of_type("fasta"):
                #set $reference_fasta_filename = "localref.fa"
            #elif $reference_source.database.is_of_type("twobit"):
                #set $reference_fasta_filename = "localref.2bit"
            #else
                #set $reference_fasta_filename = "localref"
            #end if

            ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
      #else:
            #set $reference_fasta_filename = str($reference_source.database.fields.path)
      #end if

      blat

            -q=$query_type
            -t=$database_type

            #if $oneOff
              -oneOff=1
            #end if

            #if str($minScore)
              -minScore=${minScore}
            #end if

            -maxGap=${maxGap}

            #if str($repMatch)
              -repMatch=${repMatch}
            #end if

            #if $mask_type.mask == "file.out":
                  -mask='${mask_type.mask_file}'
            #else:
                  -mask=$mask_type.mask
            #end if

            #if str($dots)
              -dots=${dots}
            #end if

            ${trimT}
            ${noTrimA}
            ${trimHardA}
            ${fastMap}
            ${fine}

            #if str($maxIntron)
             -maxIntron=${maxIntron}
            #end if

            ${extendThroughN}

            '$reference_fasta_filename'
            '${query}'

            -out=${out}

            '${output}'
]]></command>
      <inputs>
            <conditional name="reference_source">
{'fraction_non_alphanumeric': 0.12841796875, 'fraction_numerical': 0.00439453125, 'mean_word_length': 1.639819587628866, 'pattern_counts': {'":': 4, '<': 29, '<?xml version=': 2, '>': 29, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 2}, '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': '4520321', 'n_tokens_mistral': 1205, 'n_tokens_neox': 1146, 'n_words': 212}