Mercurial > repos > iuc > pilon

annotate pilon.xml @ 5:ea4a63fafc01 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 07:59:20 +0000
parents 57cfa19f44ba
children
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57cfa19f44ba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit f11cbbf24637c96c53e4a1ea5ace4b21e116677c
iuc
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1 <tool id="pilon" name="pilon" version="1.20.1">
0
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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2 <description>An automated genome assembly improvement and variant detection tool</description>
5
ea4a63fafc01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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3 <xrefs>
ea4a63fafc01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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4 <xref type="bio.tools">pilon</xref>
ea4a63fafc01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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5 </xrefs>
0
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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6 <requirements>
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ea4a63fafc01 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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7 <requirement type="package" version="1.20">pilon</requirement>
0
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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8 </requirements>
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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9 <command detect_errors="exit_code"><![CDATA[
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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10 #if $auto_selection.auto_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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11 #for $bamfile in $auto_selection.bam
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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12 ln -f -s "$bamfile" "\$(basename $bamfile)" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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13 ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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14 #end for
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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15 #end if
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16 #if $options.selection_mode == "advanced"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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17 #if $options.frags_selection.frags_enabled == "yes"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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18 #for $bamfile in $options.frags_selection.frags
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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19 ln -f -s "$bamfile" "\$(basename $bamfile)" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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20 ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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21 #end for
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22 #end if
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23 #if $options.jumps_selection.jumps_enabled == "yes"
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24 #for $bamfile in $options.jumps_selection.jumps
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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25 ln -f -s "$bamfile" "\$(basename $bamfile)" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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26 ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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27 #end for
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28 #end if
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29 #if $options.unpaired_selection.unpaired_enabled == "yes"
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30 #for $bamfile in $options.unpaired_selection.unpaired
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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31 ln -f -s "$bamfile" "\$(basename $bamfile)" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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32 ln -f -s "$bamfile.metadata.bam_index" "\$(basename $bamfile).bai" &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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33 #end for
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34 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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35 #end if
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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36 ln -s -f
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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37 #if $reference_genome.reference_genome_source == "history"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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38 "$reference_genome.history_item"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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39 #else
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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40 "$reference_genome.builtin.fields.path"
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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41 #end if
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42 reference.fasta &&
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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43 pilon
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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44 --genome reference.fasta
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45 $variant
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46 $changes
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47 #if $auto_selection.auto_enabled == "yes"
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48 #for $bamfile in $auto_selection.bam
b362b0f74c78 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit e01d50f8aa0f9a06dcf162ff6ac7d447c69a2324
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49 --bam "\$(basename $bamfile)"
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50 #end for
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51 #end if
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52 #if $options.selection_mode == "advanced"
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53 #if $options.frags_selection.frags_enabled == "yes"
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54 #for $bamfile in $options.frags_selection.frags
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55 --frags "\$(basename $bamfile)"
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56 #end for
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57 #end if
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58 #if $options.jumps_selection.jumps_enabled == "yes"
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59 #for $bamfile in $options.jumps_selection.jumps
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60 --jumps "\$(basename $bamfile)"
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61 #end for
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62 #end if
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63 #if $options.unpaired_selection.unpaired_enabled == "yes"
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64 #for $bamfile in $options.unpaired_selection.unpaired
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65 --unpaired "\$(basename $bamfile)"
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66 #end for
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67 #end if
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68 $options.vcfqe
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69 $options.vcf
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70 $options.tracks
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71 --chunksize $options.chunk_size
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72 $options.diploid
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73 $options.duplicates
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74 $options.iupac
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75 $options.nonpf
4
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76 #if len($options.targets.strip()) > 0
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77 --targets $options.targets
0
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78 #end if
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79 --fix $options.fixes
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80 $options.verbose
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81 --defaultqual $options.defaultqual
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82 --flank $options.flank
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83 --gapmargin $options.gapmargin
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84 --K $options.kmersize
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85 --mindepth $options.mindepth
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86 --mingap $options.mingap
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87 --minmq $options.minmq
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88 --minqual $options.minqual
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89 $options.nostrays
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90 #end if
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91 --threads \${GALAXY_SLOTS:-1}
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92 --output pilon
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93 ]]></command>
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94 <inputs>
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95 <conditional name="reference_genome">
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96 <param label="Source for reference genome used for BAM alignments" name="reference_genome_source" type="select">
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97 <option selected="True" value="history">Use a genome from history</option>
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98 <option value="builtin">Use a built-in genome"</option>
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99 </param>
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100 <when value="history">
4
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101 <param format="fasta" type="data" name="history_item" label="Select a reference genome"/>
0
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102 </when>
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103 <when value="builtin">
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104 <param label="Select a reference genome" name="builtin" type="select">
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105 <options from_data_table="all_fasta">
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106 <filter column="2" type="sort_by" />
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107 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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108 </options>
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109 </param>
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110 </when>
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111 </conditional>
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112 <conditional name="auto_selection">
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113 <param name="auto_enabled" label="Type automatically determined by pilon"
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114 type="boolean" checked="true" truevalue="yes" falsevalue="no" />
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115 <when value="yes">
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116 <param argument="bam" label="Input BAM file" multiple="true" type="data" format="bam"/>
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117 </when>
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118 <when value="no"></when>
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119 </conditional>
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120 <param argument="variant" type="boolean" label="Variant calling mode" checked="true" truevalue="--variant" falsevalue=""
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121 help="Sets up heuristics for variant calling, as opposed to assembly improvement; equivalent to '--vcf --fix all,breaks'."/>
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122 <param argument="changes" type="boolean" label="Create changes file" truevalue="--changes" falsevalue=""
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123 help="If specified, a file listing changes in the &lt;output&gt;.fasta will be generated."/>
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124 <conditional name="options">
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125 <param label="Use advanced options" name="selection_mode" type="select">
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126 <option selected="True" value="default">Use default options</option>
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127 <option value="advanced">Use advanced options</option>
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128 </param>
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129 <when value="default"> </when>
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130 <when value="advanced">
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131 <conditional name="frags_selection">
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132 <param name="frags_enabled" label="Paired end fragments" type="boolean" truevalue="yes" falsevalue="no" />
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133 <when value="yes">
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134 <param argument="frags" label="Input BAM file (paired end fragments)" multiple="true" type="data" format="bam"
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135 help="BAM file consisting of fragment paired-end alignments." />
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136 </when>
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137 <when value="no"></when>
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138 </conditional>
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139 <conditional name="jumps_selection">
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140 <param name="jumps_enabled" label="Mate pairs" type="boolean" truevalue="yes" falsevalue="no" />
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141 <when value="yes">
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142 <param argument="jumps" label="Input BAM file (mate pairs)" multiple="true" type="data" format="bam"
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143 help="BAM file consisting of jump (mate pair) paired-end alignments." />
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144 </when>
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145 <when value="no"></when>
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146 </conditional>
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147 <conditional name="unpaired_selection">
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148 <param name="unpaired_enabled" label="Unpaired reads" type="boolean" truevalue="yes" falsevalue="no" />
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149 <when value="yes">
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150 <param argument="unpaired" label="Input BAM file (unpaired)" multiple="true" type="data" format="bam"
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151 help="BAM file consisting of unpaired alignments." />
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152 </when>
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153 <when value="no"></when>
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154 </conditional>
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155 <param argument="vcf" type="boolean" checked="false" label="VCF output"
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156 truevalue="--vcf" falsevalue="" help="If specified, a vcf file will be generated (even if 'Variant calling mode' is off)"/>
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157 <param argument="tracks" type="boolean" checked="false" label="Output annotation tracks"
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158 help="Write many track files (*.bed, *.wig) suitable for viewing in a genome browser."
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159 truevalue="--tracks" falsevalue="" />
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160 <param argument="chunk_size" type="integer" min="1" value="10000000" label="Chunk size"
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161 help="Input FASTA elements larger than this will be processed in smaller pieces not to
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162 exceed this size." />
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163 <param argument="vcfqe" type="boolean" checked="false" label="QE (not QP) in VCF" help="If specified the VCF will contain a QE (quality-weighted evidence) field rather
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164 than the default QP (quality-weighted percentage of evidence) field." truevalue="--vcfqe" falsevalue="" />
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165 <param argument="fixes" label="Issues that pilon should try and fix" type="select" multiple="true">
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166 <option value="all" selected="true">All non-experimental fixes</option>
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167 <option value="bases">Individual bases and small indels</option>
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168 <option value="gaps">Fill gaps</option>
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169 <option value="local">Detect and fix local misassemblies</option>
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170 <option value="none">Do none of these fixes (no FASTA will be written)</option>
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171 <option value="amb">Fix ambigious bases in FASTA output (experimental)</option>
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172 <option value="breaks">Allow local reassembly to open new gaps (experimental, requires local assembly fixing to be selected)</option>
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173 <option value="novel">Assemble novel sequence from unaligned non-jump reads (experimental)</option>
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174 <!-- TODO: enable this when documented in pilon <option value="circle">Trim long reads for circular continuity(experimental, requires unpaired reads)</option>-->
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175 </param>
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176 <param argument="diploid" label="Organism is diploid" type="boolean" checked="false"
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177 help="Sample is from diploid organism; will eventually affect calling of heterozygous SNPs"
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178 truevalue="--diploid" falsevalue="" />
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179 <param argument="duplicates" label="Use duplicates" type="boolean" checked="false"
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180 help="Use reads marked as duplicates in the input BAMs"
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181 truevalue="--duplicates" falsevalue="" />
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182 <param argument="iupac" label="Use IUPAC codes in FASTA output" type="boolean" checked="false"
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183 help="Output IUPAC ambiguous base codes in the output FASTA file when appropriate"
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184 truevalue="--iupac" falsevalue="" />
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185 <param argument="nonpf" label="Use low quality reads" type="boolean" checked="false"
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186 help="Use reads which failed sequencer quality filtering"
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187 truevalue="--nonpf" falsevalue="" />
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188 <param argument="targets" label="List of targets to process (leave blank for all)" type="text"
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189 help="Only process the specified target(s). Targets are comma-separated, and each target is a fasta element name optionally followed by a base range." />
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190 <param argument="verbose" label="Verbose output (in tool log)" type="boolean" checked="false"
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191 truevalue="--verbose" falsevalue="" />
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192 <param argument="defaultqual" label="Default base quality" type="integer" min="1" value="15"
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193 help="Assumes bases are of this quality if quals are no present in input BAMs" />
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194 <param argument="flank" label="Flanking bases to ignore" type="integer" min="1" value="10"
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195 help="This many bases at each end of the good reads will be ignored." />
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196 <param argument="gapmargin" label="Allowable gap margin" type="integer" min="1" value="100000"
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197 help="Closed gaps must be within this number of bases of true size to be closed" />
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198 <param argument="kmersize" label="Kmer size" type="integer" min="1" value="47"
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199 help="Kmer size used by internal assembler" />
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200 <param argument="mindepth" label="Minimum depth" type="float" value="0.1"
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201 help="Minimum depth of coverage required for variants to be called. See complete documentation below." />
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202 <param argument="mingap" label="Mininum gap size" type="integer" value="10"
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203 help="Minimum size for unclosed gaps" />
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204 <param argument="minmq" label="Minimum mapping quality" type="integer" value="0"
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205 help="Minimum alignment mapping quality for a read to count in pileups" />
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206 <param argument="minqual" label="Minimum base quality" type="integer" value="0"
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207 help="Minimum base quality to consider for pileups" />
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208 <param argument="nostrays" label="Disable 'stray read filtering'" type="boolean" checked="false"
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209 help="See documentation below"
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210 truevalue="--nostrays" falsevalue="" />
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211 </when>
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212 </conditional>
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213 </inputs>
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214 <outputs>
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215 <data format="vcf" from_work_dir="pilon.vcf" label="VCF from ${tool.name} on ${on_string}" name="output_vcf">
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216 <filter>variant or (options['selection_mode'] == 'advanced' and options['vcf'])</filter>
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217 </data>
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218 <data format="txt" from_work_dir="pilon.changes" label="Changes in FASTA from ${tool.name} on ${on_string}" name="output_changes">
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219 <filter>changes</filter>
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220 </data>
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221 <data format="fasta" from_work_dir="pilon.fasta" label="FASTA from ${tool.name} on ${on_string}" name="output_fasta">
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222 <filter>options['selection_mode'] == 'default' or (options['selection_mode'] == 'advanced' and 'none' not in options['fixes'])</filter>
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223 </data>
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224 <collection name="tracks" type="list" label="Annotation tracks from ${tool.name} on ${on_string}">
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225 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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226 <data format="bed" from_work_dir="pilonPilon.bed" label="Features from ${tool.name} on ${on_string} (BED format)" name="output_pilon_bed" />
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227 <data format="wig" from_work_dir="pilonChanges.wig" label="${tool.name} changes track on ${on_string} (WIG format)" name="output_changes_wig" />
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228 <data format="wig" from_work_dir="pilonUnconfirmed.wig" label="${tool.name} unconfirmed track on ${on_string}" name="output_unconfirmed_wig" />
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229 <data format="wig" from_work_dir="pilonCopyNumber.wig" label="${tool.name} copy number track on ${on_string}" name="output_copynumber_wig" />
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230 <data format="wig" from_work_dir="pilonCoverage.wig" label="${tool.name} coverage track on ${on_string}" name="output_coverage_wig" />
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231 <data format="wig" from_work_dir="pilonBadCoverage.wig" label="${tool.name} bad coverage track on ${on_string}" name="output_badcoverage_wig" />
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232 <data format="wig" from_work_dir="pilonPctBad.wig" label="${tool.name} pct bad track on ${on_string}" name="output_pctbad_wig" />
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233 <data format="wig" from_work_dir="pilonDeltaCoverage.wig" label="${tool.name} delta coverage track on ${on_string}" name="output_deltacoverage_wig" />
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234 <data format="wig" from_work_dir="pilonDipCoverage.wig" label="${tool.name} dip coverage track on ${on_string}" name="output_dipcoverage_wig" />
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235 <data format="wig" from_work_dir="pilonPhysicalCoverage.wig" label="${tool.name} physical coverage track on ${on_string}" name="output_physicalcoverage_wig" />
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236 <data format="wig" from_work_dir="pilonClippedAlignments.wig" label="${tool.name} clipped alignments track on ${on_string}" name="output_clippedalignments_wig" />
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237 <data format="wig" from_work_dir="pilonWeightedQual.wig" label="${tool.name} weighted quality track on ${on_string}" name="output_weightedqual_wig" />
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238 <data format="wig" from_work_dir="pilonWeightedMq.wig" label="${tool.name} weighted MQ track on ${on_string}" name="output_weightedmq_wig" />
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239 <data format="wig" from_work_dir="pilonGC.wig" label="${tool.name} GC track on ${on_string}" name="output_gc_wig" />
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240 </collection>
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241 </outputs>
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242 <tests>
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243 <test>
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244 <param name="reference_genome_source" value="history" />
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245 <param ftype="fasta" name="history_item" value="test1.fasta" />
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246 <param name="bam" value="test1.bam" />
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247 <param name="variant" value="true" />
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248 <output file="test1-vcf-part" ftype="vcf" name="output_vcf" compare="contains" />
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249 <output md5="352907b0d965bc926289b1b2eb9cbecb" ftype="fasta" name="output_fasta" />
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250 </test>
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251 <test>
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252 <param name="reference_genome_source" value="history" />
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253 <param ftype="fasta" name="history_item" value="test1.fasta" />
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254 <param name="bam" value="test1.bam" />
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255 <param name="variant" value="true" />
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256 <param name="selection_mode" value="advanced" />
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257 <param name="tracks" value="true" />
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258 <output file="test1-vcf-part" ftype="vcf" name="output_vcf" compare="contains" />
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259 <output md5="352907b0d965bc926289b1b2eb9cbecb" ftype="fasta" name="output_fasta" />
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260 <output_collection name="tracks">
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261 <element name="output_pilon_bed" md5="ae0518a6d641efecdcf41c808c014226" />
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262 <element name="output_changes_wig" md5="26e0a9a3793e6604673e9911c4d334ab" />
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263 <element name="output_unconfirmed_wig" md5="f8bb3def4547e854bd90e1a6b4f8cc66" />
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264 <element name="output_copynumber_wig" md5="c1e94296fbc24d00fa7d057f30e4de8f" />
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265 <element name="output_coverage_wig" md5="48f7da4bad60fcbb49aaaa992aef8a02" />
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266 <element name="output_badcoverage_wig" md5="31e3ad4a5d0f8cd1e296e4b1424d6a95" />
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267 <element name="output_pctbad_wig" md5="8353134113c87dbc7d9497f983d58b4b" />
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268 <element name="output_deltacoverage_wig" md5="e0fb6474b851e1890f91c57c2ba1fd76" />
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269 <element name="output_dipcoverage_wig" md5="8885c63df1dc7309a7bab371b9eb449b" />
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270 <element name="output_physicalcoverage_wig" md5="db485f84b51499c3a3c72da70a8ef7af" />
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271 <element name="output_clippedalignments_wig" md5="b6eab0827a9b6f2e925d9ece5ee4f87f" />
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272 <element name="output_weightedqual_wig" md5="9987289bd0ec8cd05bd6d330bdd1d01d" />
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273 <element name="output_weightedmq_wig" md5="7ec1b6420f52fc44bf3c04aa593fcdeb" />
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274 <element name="output_gc_wig" md5="815af1378d016b85ed6f52667dde10c1" />
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275 </output_collection>
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276 </test>
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277
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278 </tests>
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279 <help><![CDATA[
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280 Pilon is a software tool which can be used to:
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281
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282 * Automatically improve draft assemblies
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283
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284 * Find variation among strains, including large event detection
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285
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286 Pilon requires as input a FASTA file of the genome along with one or more BAM files of reads aligned to the input FASTA file. Pilon uses read alignment analysis to identify inconsistencies between the input genome and the evidence in the reads. It then attempts to make improvements to the input genome, including:
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287
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288 * Single base differences
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289
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290 * Small indels
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291
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292 * Larger indel or block substitution events
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293
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294 * Gap filling
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295
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296 * Identification of local misassemblies, including optional opening of new gaps
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297
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298 Pilon then outputs a FASTA file containing an improved representation of the genome from the read data and an optional VCF file detailing variation seen between the read data and the input genome.
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299
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300 To aid manual inspection and improvement by an analyst, Pilon can optionally produce tracks that can be displayed in genome viewers such as IGV and GenomeView, and it reports other events (such as possible large collapsed repeat regions) in its standard output.
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301
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302 Note on **mindepth**:
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303
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304 Variants (snps and indels) will only be called if there is coverage of good pairs
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305 at the value set for *mindepth* depth or more; if this value is >= 1, it is an absolute depth, if it is a
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306 fraction < 1, then minimum depth is computed by multiplying this value by the mean
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307 coverage for the region, with a minumum value of 5 (default 0.1: min depth to call
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308 is 10% of mean coverage or 5, whichever is greater).
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309
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310 Note on **stray read filtering**
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311
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312 By default a pass is made through the input BAM files to identify stray pairs, that is,
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313 those pairs in which both reads are aligned but not marked valid because they have
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314 inconsistent orientation or separation. Identifying stray pairs can help fill gaps
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315 and assemble larger insertions, especially of repeat content. However, doing so
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316 sometimes consumes considerable memory.
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317 ]]></help>
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318 <citations>
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319 <citation type="doi">10.1371/journal.pone.0112963</citation>
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320 </citations>
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321 </tool>