<commit_before><tool id="smalt_map" name="smalt map" version="1.2.0" >
    <description>Map query reads (FASTA/FASTQ) format onto the reference sequences</description>
    <requirements>
        <requirement type="package" version="0.7.6">smalt</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"   level="fatal"   description="Unknown error" />
        <regex match="Command line error"
               source="stdout"
               level="fatal"
               description="You cannot do that!! What were you thinking!" />
        <regex match="ERROR"
               source="stderr"
               level="fatal"
               description="You cannot do that!! What were you thinking!" />
    </stdio>
    <command>
        smalt_map.sh $smi $sma $oformat.outformat

        #if $singlePaired.sPaired == "single":
              1 $singlePaired.sInput1
        #elif $singlePaired.sPaired == "paired":<commit_msg>added tool directory path variable so we can find the smalt.sh script<commit_after><tool id="smalt_map" name="smalt map" version="1.2.0" >
    <description>Map query reads (FASTA/FASTQ) format onto the reference sequences</description>
    <requirements>
        <requirement type="package" version="0.7.6">smalt</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"   level="fatal"   description="Unknown error" />
        <regex match="Command line error"
               source="stdout"
               level="fatal"
               description="You cannot do that!! What were you thinking!" />
        <regex match="ERROR"
               source="stderr"
               level="fatal"
               description="You cannot do that!! What were you thinking!" />
    </stdio>
    <command>
        bash $__tool_directory__/smalt_map.sh $smi $sma $oformat.outformat

        #if $singlePaired.sPaired == "single":
              1 $singlePaired.sInput1
        #elif $singlePaired.sPaired == "paired":
{'fraction_non_alphanumeric': 0.1251916198262647, 'fraction_numerical': 0.009197751660705161, 'mean_word_length': 2.45326278659612, 'pattern_counts': {'":': 4, '<': 29, '<?xml version=': 0, '>': 29, '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': '1757983', 'n_tokens_mistral': 564, 'n_tokens_neox': 546, 'n_words': 145}