<commit_before><tool id="seqwish" name="seqwish" version="@TOOL_VERSION@" >
    <description>Alignment to variation graph inducer</description>
    <macros>
        <token name="@TOOL_VERSION@">0.4</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">seqwish</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
seqwish
-p '$paf_alns'
-s ${ ' '.join(["'%s'" % x for x in $seqs]) }
--gfa='$out_gfa'
#if $m:
    -m '$m'
#end if
--threads=\${GALAXY_SLOTS:-1}
#if str($r):
    -r $r
#end if
#if str($k):
    -k $k
#end if
#if str($B):
    -B $B
#end if
    ]]></command>
    <inputs>
        <param argument="--paf-alns" type="data" format="paf" label="Induce the graph from these PAF formatted alignments" />
        <param argument="--seqs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="The sequences used to generate the alignments" />
        <param argument="-m" type="data" optional="true" format="txt,tabular" label="Subset the input alignments"
            help="" />
        <param argument="-r" type="integer" min="1" optional="true" label="Limit copies of a given input base"
            help="Limit transitive closure to include no more than N copies of a given input base" />
        <param argument="-k" type="integer" min="1" optional="true" label="Filter exact matches below this length"
            help="This can smooth the graph locally and prevent the formation of complex local graph topologies from forming due to differential alignments." />
        <param argument="-B" type="integer" min="1" optional="true" label="Number of bp to use for transitive closure batch"
            help="" />
    </inputs>

    <outputs>
        <data name="out_gfa" format="gfa" label="${tool.name} on ${on_string}" />
    </outputs>
<commit_msg>Rename output format to gfa1<commit_after><tool id="seqwish" name="seqwish" version="@TOOL_VERSION@" >
    <description>Alignment to variation graph inducer</description>
    <macros>
        <token name="@TOOL_VERSION@">0.4</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">seqwish</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
seqwish
-p '$paf_alns'
-s ${ ' '.join(["'%s'" % x for x in $seqs]) }
--gfa='$out_gfa'
#if $m:
    -m '$m'
#end if
--threads=\${GALAXY_SLOTS:-1}
#if str($r):
    -r $r
#end if
#if str($k):
    -k $k
#end if
#if str($B):
    -B $B
#end if
    ]]></command>
    <inputs>
        <param argument="--paf-alns" type="data" format="paf" label="Induce the graph from these PAF formatted alignments" />
        <param argument="--seqs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="The sequences used to generate the alignments" />
        <param argument="-m" type="data" optional="true" format="txt,tabular" label="Subset the input alignments"
            help="" />
        <param argument="-r" type="integer" min="1" optional="true" label="Limit copies of a given input base"
            help="Limit transitive closure to include no more than N copies of a given input base" />
        <param argument="-k" type="integer" min="1" optional="true" label="Filter exact matches below this length"
            help="This can smooth the graph locally and prevent the formation of complex local graph topologies from forming due to differential alignments." />
        <param argument="-B" type="integer" min="1" optional="true" label="Number of bp to use for transitive closure batch"
            help="" />
    </inputs>

    <outputs>
        <data name="out_gfa" format="gfa1" label="${tool.name} on ${on_string}" />
    </outputs>

{'fraction_non_alphanumeric': 0.16165413533834586, 'fraction_numerical': 0.0037593984962406013, 'mean_word_length': 3.515151515151515, 'pattern_counts': {'":': 0, '<': 53, '<?xml version=': 0, '>': 53, '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': '1175162', 'n_tokens_mistral': 1189, 'n_tokens_neox': 1156, 'n_words': 354}