<commit_before><tool id="pilon" name="pilon" version="1.20.0">
    <description>An automated genome assembly improvement and variant detection tool</description>
    <requirements>
      <requirement type="package" version="1.20">pilon</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if $auto_selection.auto_enabled == "yes"
        #for $bamfile in $auto_selection.bam
          ln -f -s "$bamfile" "\$(basename $bamfile)" &&
          ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
        #end for
      #end if
      #if $options.selection_mode == "advanced"
        #if $options.frags_selection.frags_enabled == "yes"
          #for $bamfile in $options.frags_selection.frags
            ln -f -s "$bamfile" "\$(basename $bamfile)" &&
            ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
          #end for
        #end if
        #if $options.jumps_selection.jumps_enabled == "yes"
         #for $bamfile in $options.jumps_selection.jumps
           ln -f -s "$bamfile" "\$(basename $bamfile)" &&
           ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
         #end for
        #end if
        #if $options.unpaired_selection.unpaired_enabled == "yes"
          #for $bamfile in $options.unpaired_selection.unpaired
            ln -f -s "$bamfile" "\$(basename $bamfile)" &&
            ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
          #end for
        #end if
      #end if
        ln -s -f
          #if $reference_genome.reference_genome_source == "history"
            "$reference_genome.history_item"
          #else
            "$reference_genome.builtin.fields.path"
          #end if
          reference.fasta &&
        pilon
        --genome reference.fasta
        $variant
        $changes
        #if $auto_selection.auto_enabled == "yes"
          #for $bamfile in $auto_selection.bam
            --bam "\$(basename $bamfile)"
          #end for
        #end if
        #if $options.selection_mode == "advanced"
          #if $options.frags_selection.frags_enabled == "yes"
            #for $bamfile in $options.frags_selection.frags
              --frags "\$(basename $bamfile)"
            #end for
          #end if
          #if $options.jumps_selection.jumps_enabled == "yes"
            #for $bamfile in $options.jumps_selection.jumps
              --jumps "\$(basename $bamfile)"
            #end for
          #end if
          #if $options.unpaired_selection.unpaired_enabled == "yes"
            #for $bamfile in $options.unpaired_selection.unpaired
              --unpaired "\$(basename $bamfile)"
            #end for
          #end if
          $options.vcfqe
          $options.vcf
          $options.tracks
          --chunksize $options.chunk_size
          $options.diploid
          $options.duplicates
          $options.iupac
          $options.nonpf
          #if len($options.targetlist.strip()) > 0
            --targetlist $options.targetlist
          #end if
          --fix $options.fixes
          $options.verbose
          --defaultqual $options.defaultqual
          --flank $options.flank
          --gapmargin $options.gapmargin
          --K $options.kmersize
          --mindepth $options.mindepth
          --mingap $options.mingap
          --minmq $options.minmq
          --minqual $options.minqual
          $options.nostrays
        #end if
        --threads \${GALAXY_SLOTS:-1}<commit_msg>Pilon - fix targetlist argument<commit_after><tool id="pilon" name="pilon" version="1.20.0">
    <description>An automated genome assembly improvement and variant detection tool</description>
    <requirements>
      <requirement type="package" version="1.20">pilon</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if $auto_selection.auto_enabled == "yes"
        #for $bamfile in $auto_selection.bam
          ln -f -s "$bamfile" "\$(basename $bamfile)" &&
          ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
        #end for
      #end if
      #if $options.selection_mode == "advanced"
        #if $options.frags_selection.frags_enabled == "yes"
          #for $bamfile in $options.frags_selection.frags
            ln -f -s "$bamfile" "\$(basename $bamfile)" &&
            ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
          #end for
        #end if
        #if $options.jumps_selection.jumps_enabled == "yes"
         #for $bamfile in $options.jumps_selection.jumps
           ln -f -s "$bamfile" "\$(basename $bamfile)" &&
           ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
         #end for
        #end if
        #if $options.unpaired_selection.unpaired_enabled == "yes"
          #for $bamfile in $options.unpaired_selection.unpaired
            ln -f -s "$bamfile" "\$(basename $bamfile)" &&
            ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
          #end for
        #end if
      #end if
        ln -s -f
          #if $reference_genome.reference_genome_source == "history"
            "$reference_genome.history_item"
          #else
            "$reference_genome.builtin.fields.path"
          #end if
          reference.fasta &&
        pilon
        --genome reference.fasta
        $variant
        $changes
        #if $auto_selection.auto_enabled == "yes"
          #for $bamfile in $auto_selection.bam
            --bam "\$(basename $bamfile)"
          #end for
        #end if
        #if $options.selection_mode == "advanced"
          #if $options.frags_selection.frags_enabled == "yes"
            #for $bamfile in $options.frags_selection.frags
              --frags "\$(basename $bamfile)"
            #end for
          #end if
          #if $options.jumps_selection.jumps_enabled == "yes"
            #for $bamfile in $options.jumps_selection.jumps
              --jumps "\$(basename $bamfile)"
            #end for
          #end if
          #if $options.unpaired_selection.unpaired_enabled == "yes"
            #for $bamfile in $options.unpaired_selection.unpaired
              --unpaired "\$(basename $bamfile)"
            #end for
          #end if
          $options.vcfqe
          $options.vcf
          $options.tracks
          --chunksize $options.chunk_size
          $options.diploid
          $options.duplicates
          $options.iupac
          $options.nonpf
          #if len($options.targetlist.strip()) > 0
            --targets $options.targetlist
          #end if
          --fix $options.fixes
          $options.verbose
          --defaultqual $options.defaultqual
          --flank $options.flank
          --gapmargin $options.gapmargin
          --K $options.kmersize
          --mindepth $options.mindepth
          --mingap $options.mingap
          --minmq $options.minmq
          --minqual $options.minqual
          $options.nostrays
        #end if
        --threads \${GALAXY_SLOTS:-1}
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{'dir': 'git-commits-cleaned', 'id': '6473271', 'n_tokens_mistral': 2231, 'n_tokens_neox': 2168, 'n_words': 468}