<commit_before><tool id="arriba" name="Arriba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>detect gene fusions from STAR aligned RNA-Seq data</description>
    <macros>
        <import>macros.xml</import>
        <xml name="fusion_actions">
            <actions>
                <action name="comment_lines" type="metadata" default="1" />
                <action name="column_names" type="metadata" default="gene1,gene2,strand1(gene/fusion),strand2(gene/fusion),breakpoint1,breakpoint2,site1,site2,type,split_reads1,split_reads2,discordant_mates,coverage1,coverage2,confidence,reading_frame,tags,retained_protein_domains,closest_genomic_breakpoint1,closest_genomic_breakpoint2,gene_id1,gene_id2,transcript_id1,transcript_id2,direction1,direction2,filters,fusion_transcript,peptide_sequence,read_identifiers" />
            </actions>
        </xml>
        <token name="@VIRAL_CONTIG@">([AN]C_([*]|\d+))</token>
        <token name="@GENOME_CONTIG@">((chr)?(\d|\d\d|X|Y|M(t)?))</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
@GENOME_SOURCE@
@GTF_SOURCE@
#set $filter_list = []
#if $options.filters
    #set $filter_list = $options.filters.split(',')
#end if
#if $blacklist
    #if $blacklist.is_of_type('tabular.gz')
        #set $blacklist_file = 'blacklist.tsv.gz'
        ln -sf '$blacklist'  $blacklist_file &&
    #else
        #set $blacklist_file = $blacklist
    #end if
#else
    #if 'blacklist' not in $filter_list
        #silent $filter_list.append('blacklist')
    #end if
#end if
#set $filters = ','.join($filter_list) 
#if $known_fusions
    #if $known_fusions.is_of_type('tabular.gz')
        #set $known_fusions_file = 'known_fusions.tsv.gz'
        ln -sf '$known_fusions'  $known_fusions_file &&
    #else
        #set $known_fusions_file = $known_fusions
    #end if
#end if
#if $tags
    #if $tags.is_of_type('tabular.gz')
        #set $tags_file = 'tags.tsv.gz'
        ln -sf '$tags'  $tags_file &&
    #else
        #set $tags_file = $tags
    #end if
#end if
     arriba 
    -x '$input'
    #if $chimeric
        -c '$chimeric'
    #end if
    -a '$genome_assembly'
    -g 'genome.gtf'
    #if $blacklist
        -b '$blacklist_file'
    #end if
    #if $filters
        -f '$filters'
    #end if
    #if $protein_domains
        -p '$protein_domains'
    #end if
    #if $known_fusions
        -k '$known_fusions_file'
    #end if
    #if $tags
        -t '$tags_file'
    #end if
    #if str($wgs_cond.use_wgs) == "yes"
        -d '$wgs_cond.wgs'
        #if str($wg_cond.max_genomic_breakpoint_distance)
            -D $wgs_cond.max_genomic_breakpoint_distance
        #end if
    #end if
    -o fusions.tsv
    #if $output_fusions_discarded
    -O fusions.discarded.tsv 
    #end if
    ## Arriba options
    #if $options.gtf_features
        -G '$options.gtf_features'
    #end if
    #if $options.strandedness
        -s $options.strandedness
    #end if<commit_msg>Fix typo Arriba<commit_after><tool id="arriba" name="Arriba" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
    <description>detect gene fusions from STAR aligned RNA-Seq data</description>
    <macros>
        <import>macros.xml</import>
        <xml name="fusion_actions">
            <actions>
                <action name="comment_lines" type="metadata" default="1" />
                <action name="column_names" type="metadata" default="gene1,gene2,strand1(gene/fusion),strand2(gene/fusion),breakpoint1,breakpoint2,site1,site2,type,split_reads1,split_reads2,discordant_mates,coverage1,coverage2,confidence,reading_frame,tags,retained_protein_domains,closest_genomic_breakpoint1,closest_genomic_breakpoint2,gene_id1,gene_id2,transcript_id1,transcript_id2,direction1,direction2,filters,fusion_transcript,peptide_sequence,read_identifiers" />
            </actions>
        </xml>
        <token name="@VIRAL_CONTIG@">([AN]C_([*]|\d+))</token>
        <token name="@GENOME_CONTIG@">((chr)?(\d|\d\d|X|Y|M(t)?))</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code"><![CDATA[
@GENOME_SOURCE@
@GTF_SOURCE@
#set $filter_list = []
#if $options.filters
    #set $filter_list = $options.filters.split(',')
#end if
#if $blacklist
    #if $blacklist.is_of_type('tabular.gz')
        #set $blacklist_file = 'blacklist.tsv.gz'
        ln -sf '$blacklist'  $blacklist_file &&
    #else
        #set $blacklist_file = $blacklist
    #end if
#else
    #if 'blacklist' not in $filter_list
        #silent $filter_list.append('blacklist')
    #end if
#end if
#set $filters = ','.join($filter_list) 
#if $known_fusions
    #if $known_fusions.is_of_type('tabular.gz')
        #set $known_fusions_file = 'known_fusions.tsv.gz'
        ln -sf '$known_fusions'  $known_fusions_file &&
    #else
        #set $known_fusions_file = $known_fusions
    #end if
#end if
#if $tags
    #if $tags.is_of_type('tabular.gz')
        #set $tags_file = 'tags.tsv.gz'
        ln -sf '$tags'  $tags_file &&
    #else
        #set $tags_file = $tags
    #end if
#end if
     arriba 
    -x '$input'
    #if $chimeric
        -c '$chimeric'
    #end if
    -a '$genome_assembly'
    -g 'genome.gtf'
    #if $blacklist
        -b '$blacklist_file'
    #end if
    #if $filters
        -f '$filters'
    #end if
    #if $protein_domains
        -p '$protein_domains'
    #end if
    #if $known_fusions
        -k '$known_fusions_file'
    #end if
    #if $tags
        -t '$tags_file'
    #end if
    #if str($wgs_cond.use_wgs) == "yes"
        -d '$wgs_cond.wgs'
        #if str($wgs_cond.max_genomic_breakpoint_distance)
            -D $wgs_cond.max_genomic_breakpoint_distance
        #end if
    #end if
    -o fusions.tsv
    #if $output_fusions_discarded
    -O fusions.discarded.tsv 
    #end if
    ## Arriba options
    #if $options.gtf_features
        -G '$options.gtf_features'
    #end if
    #if $options.strandedness
        -s $options.strandedness
    #end if
{'fraction_non_alphanumeric': 0.14063268316669397, 'fraction_numerical': 0.008195377806916898, 'mean_word_length': 3.0761523046092183, 'pattern_counts': {'":': 0, '<': 45, '<?xml version=': 0, '>': 43, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 6}, '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': '5251646', 'n_tokens_mistral': 2300, 'n_tokens_neox': 2202, 'n_words': 399}