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annotate pilon.xml @ 3:0620d04a705c draft default tip

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit c8d758be3636220bebe4b72e680b57d327fcc96d
author sanbi-uwc
date Thu, 11 Aug 2016 12:50:15 -0400
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eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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1 <tool id="pilon" name="pilon" version="0.1">
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2 <description>An automated genome assembly improvement and variant detection tool</description>
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3 <requirements>
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4 <requirement type="package" version="1.18">pilon</requirement>
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5 <!--<requirement type="set_environment">CLASSPATH</requirement>-->
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6 <!-- if CLASSPATH is set to include pilon jar, you can call pilon with
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7 java com.simontuffs.onejar.Boot -->>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 </stdio>
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12 <command><![CDATA[
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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13 #for $input_bam in $input_bams
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14 ln -f -s "${input_bam.metadata.bam_index}" "${input_bam}.bai" &&
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15 #end for
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16 #if $options.selection_mode == "advanced"
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17 #for $bam in $options.input_frag_bams + $options.input_jump_bams + $options.input_unpaired_bams
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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18 ln -s -f "${bam.metadata.bam_index}" "${bam}.bai" &&
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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19 #end for
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20 #end if
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21 ln -s -f
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22 #if $reference_genome.reference_genome_source == "history"
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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23 $reference_genome.history_item
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24 #else
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25 $reference_genome.builtin.fields.path
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26 #end if
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27 reference.fasta &&
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28 pilon
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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29 --genome reference.fasta
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30 #for $input_bam in $input_bams
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31 --bam $input_bam
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32 #end for
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33 $variant_calling
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34 $changes
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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35 #if $options.selection_mode == "advanced"
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36 $options.vcfqe
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37 $options.vcf_output
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38 $options.tracks
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39 --chunksize $options.chunk_size
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40 $options.diploid
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41 $options.duplicates
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42 $options.iupac
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43 $options.nonpf
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44 #if len($options.targetlist.strip()) > 0
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45 --targetlist $options.targetlist
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46 #end if
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47 --fix $options.fixes
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48 $options.verbose
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49 --defaultqual $options.defaultqual
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50 --flank $options.flank
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51 --gapmargin $options.gapmargin
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52 --K $options.kmersize
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53 --mindepth $options.mindepth
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54 --mingap $options.mingap
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55 --minmq $options.minmq
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56 --minqual $options.minqual
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57 $options.nostrays
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58 #end if
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59 --threads \${GALAXY_SLOTS:-1}
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60 --output pilon &&
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61 if [ -f pilon.fasta ] ; then mv pilon.fasta $output_fasta ; fi &&
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62 if [ -f pilon.vcf ] ; then mv pilon.vcf $output_vcf ; fi &&
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63 if [ -f pilon.changes ] ; then mv pilon.changes $output_changes ; fi &&
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64 if [ -f pilonPilon.bed ] ; then mv pilonPilon.bed $output_pilon_bed ; fi &&
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65 if [ -f pilonChanges.wig ] ; then mv pilonChanges.wig $output_changes_wig ; fi &&
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66 if [ -f pilonUnconfirmed.wig ] ; then mv pilonUnconfirmed.wig $output_unconfirmed_wig ; fi &&
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67 if [ -f pilonCopyNumber.wig ] ; then mv pilonCopyNumber.wig $output_copynumber_wig ; fi &&
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68 if [ -f pilonCoverage.wig ] ; then mv pilonCoverage.wig $output_coverage_wig ; fi &&
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69 if [ -f pilonBadCoverage.wig ] ; then mv pilonBadCoverage.wig $output_badcoverage_wig ; fi &&
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70 if [ -f pilonPctBad.wig ] ; then mv pilonPctBad.wig $output_pctbad_wig ; fi &&
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71 if [ -f pilonDeltaCoverage.wig ] ; then mv pilonDeltaCoverage.wig $output_deltacoverage_wig ; fi &&
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72 if [ -f pilonDipCoverage.wig ] ; then mv pilonDipCoverage.wig $output_dipcoverage_wig ; fi &&
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73 if [ -f pilonPhysicalCoverage.wig ] ; then mv pilonPhysicalCoverage.wig $output_physicalcoverage_wig ; fi &&
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74 if [ -f pilonClippedAlignments.wig ] ; then mv pilonClippedAlignments.wig $output_clippedalignments_wig ; fi &&
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75 if [ -f pilonWeightedQual.wig ] ; then mv pilonWeightedQual.wig $output_weightedqual_wig ; fi &&
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76 if [ -f pilonWeightedMq.wig ] ; then mv pilonWeightedMq.wig $output_weightedmq_wig ; fi &&
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77 if [ -f pilonGC.wig ] ; then mv pilonGC.wig $output_gc_wig ; fi
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78 ]]></command>
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79 <inputs>
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80 <conditional name="reference_genome">
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81 <param label="Source for reference genome used for BAM alignments" name="reference_genome_source" type="select">
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82 <option selected="True" value="history">Use a genome from history</option>
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83 <option value="builtin">Use a built-in genome"</option>
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84 </param>
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85 <when value="history">
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86 <param format="fasta" type="data" metadata_name="dbkey" name="history_item" />
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87 </when>
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88 <when value="builtin">
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89 <param label="Select a reference genome" name="builtin" type="select">
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90 <options from_data_table="all_fasta">
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91 <filter column="2" type="sort_by" />
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92 <validator message="No genomes are available for the selected input dataset" type="no_options" />
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93 </options>
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94 </param>
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95 </when>
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96 </conditional>
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97 <param label="Input BAM file" multiple="true" type="data" format="bam" name="input_bams"/>
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98 <param name="variant_calling" type="boolean" label="Variant calling mode" checked="true" truevalue="--variant" falsevalue="" />
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99 <param name="changes" type="boolean" label="Output file describing changes in FASTA output" truevalue="--changes" falsevalue="" />
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100 <conditional name="options">
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101 <param label="Use advanced options" name="selection_mode" type="select">
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102 <option selected="True" value="default">Use default options</option>
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103 <option value="advanced">Use advanced options</option>
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104 </param>
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105 <when value="default"> </when>
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106 <when value="advanced">
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107 <param name="vcf_output" type="boolean" checked="false" label="VCF output (even if 'Variant calling mode' is off)"
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108 truevalue="--vcf" falsevalue="" />
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109 <param name="tracks" type="boolean" checked="false" label="Output annotation tracks"
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110 help="Write many track files (*.bed, *.wig) suitable for viewing in a genome browser."
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111 truevalue="--tracks" falsevalue="" />
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112 <param name="chunk_size" type="integer" min="1" value="10000000" label="Chunk size"
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113 help="Input FASTA elements larger than this will be processed in smaller pieces not to
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114 exceed this size." />
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115 <param name="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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116 than the default QP (quality-weighted percentage of evidence) field." truevalue="--vcfqe" falsevalue="" />
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117 <param name="input_frag_bams" label="Input BAM file (paired end fragments)" multiple="true" type="data" format="bam"
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118 help="BAM file consisting of fragment paired-end alignments." />
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119 <param name="input_jump_bams" label="Input BAM file (mate pairs)" multiple="true" type="data" format="bam"
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120 help="BAM file consisting of jump (mate pair) paired-end alignments." />
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121 <param name="input_unpaired_bams" label="Input BAM file (unpaired)" multiple="true" type="data" format="bam"
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122 help="BAM file consisting of unpaired alignments." />
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123 <param name="fixes" label="Issues that pilon should try and fix" type="select" multiple="true">
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124 <option value="all" selected="true">All non-experimental fixes</option>
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125 <option value="bases">Individual bases and small indels</option>
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126 <option value="gaps">Fill gaps</option>
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127 <option value="local">Detect and fix local misassemblies</option>
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128 <option value="none">Do none of these fixes (no FASTA will be written)</option>
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129 <option value="amb">Fix ambigious bases in FASTA output (experimental)</option>
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130 <option value="breaks">Allow local reassembly to open new gaps (experimental, requires local assembly fixing to be selected)</option>
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131 <option value="novel">Assemble novel sequence from unaligned non-jump reads (experimental)</option>
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132 </param>
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133 <param name="diploid" label="Organism is diploid" type="boolean" checked="false"
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134 help="Sample is from diploid organism; will eventually affect calling of heterozygous SNPs"
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135 truevalue="--diploid" falsevalue="" />
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136 <param name="duplicates" label="Use duplicates" type="boolean" checked="false"
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137 help="Use reads marked as duplicates in the input BAMs"
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138 truevalue="--duplicates" falsevalue="" />
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139 <param name="iupac" label="Use IUPAC codes in FASTA output" type="boolean" checked="false"
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140 help="Output IUPAC ambiguous base codes in the output FASTA file when appropriate"
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141 truevalue="--iupac" falsevalue="" />
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142 <param name="nonpf" label="Use low quality reads" type="boolean" checked="false"
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143 help="Use reads which failed sequencer quality filtering"
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144 truevalue="--nonpf" falsevalue="" />
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145 <param name="targetlist" label="List of targets to process (leave blank for all)" default="" type="text" length="40"
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146 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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147 <param name="verbose" label="Verbose output (in tool log)" type="boolean" check="false"
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148 truevalue="--verbose" falsevalue="" />
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149 <param name="defaultqual" label="Default base quality" type="integer" min="1" value="15"
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150 help="Assumes bases are of this quality if quals are no present in input BAMs" />
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151 <param name="flank" label="Flanking bases to ignore" type="integer" min="1" value="10"
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152 help="This many bases at each end of the good reads will be ignored." />
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153 <param name="gapmargin" label="Allowable gap margin" type="integer" min="1" value="100000"
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154 help="Closed gaps must be within this number of bases of true size to be closed" />
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155 <param name="kmersize" label="Kmer size" type="integer" min="1" value="47"
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156 help="Kmer size used by internal assembler" />
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157 <param name="mindepth" label="Minimum depth" type="float" value="0.1"
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158 help="Minimum depth of coverage required for variants to be called. See complete documentation below." />
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159 <param name="mingap" label="Mininum gap size" type="integer" value="10"
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160 help="Minimum size for unclosed gaps" />
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161 <param name="minmq" label="Minimum mapping quality" type="integer" value="0"
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162 help="Minimum alignment mapping quality for a read to count in pileups" />
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163 <param name="minqual" label="Minimum base quality" type="integer" value="0"
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164 help="Minimum base quality to consider for pileups" />
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165 <param name="nostrays" label="Disable 'stray read filtering'" type="boolean" checked="false"
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166 help="See documentation below"
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167 truevalue="--nostrays" falsevalue="" />
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168 </when>
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169 </conditional>
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170 </inputs>
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171 <outputs>
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172 <data format="vcf" label="VCF from ${tool.name} on ${on_string}" name="output_vcf">
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173 <filter>variant_calling or (options['selection_mode'] == 'advanced' and options['vcf_output'])</filter>
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174 </data>
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175 <data format="txt" label="Changes in FASTA from ${tool.name} on ${on_string}" name="output_changes">
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176 <filter>changes</filter>
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177 </data>
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178 <data format="fasta" label="FASTA from ${tool.name} on ${on_string}" name="output_fasta">
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179 <filter>options['selection_mode'] == 'default' or (options['selection_mode'] == 'advanced' and 'none' not in options['fixes'])</filter>
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180 </data>
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181 <data format="bed" label="Features from ${tool.name} on ${on_string} (BED format)" name="output_pilon_bed">
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182 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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183 </data>
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184 <data format="wig" label="${tool.name} changes track on ${on_string} (WIG format)" name="output_changes_wig">
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185 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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186 </data>
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187 <data format="wig" label="${tool.name} unconfirmed track on ${on_string}" name="output_unconfirmed_wig">
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188 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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189 </data>
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190 <data format="wig" label="${tool.name} copy number track on ${on_string}" name="output_copynumber_wig">
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191 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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192 </data>
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193 <data format="wig" label="${tool.name} coverage track on ${on_string}" name="output_coverage_wig">
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194 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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195 </data>
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196 <data format="wig" label="${tool.name} bad coverage track on ${on_string}" name="output_badcoverage_wig">
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197 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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198 </data>
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199 <data format="wig" label="${tool.name} pct bad track on ${on_string}" name="output_pctbad_wig">
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200 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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201 </data>
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202 <data format="wig" label="${tool.name} delta coverage track on ${on_string}" name="output_deltacoverage_wig">
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203 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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204 </data>
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205 <data format="wig" label="${tool.name} dip coverage track on ${on_string}" name="output_dipcoverage_wig">
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206 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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207 </data>
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208 <data format="wig" label="${tool.name} physical coverage track on ${on_string}" name="output_physicalcoverage_wig">
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209 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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210 </data>
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211 <data format="wig" label="${tool.name} clipped alignments track on ${on_string}" name="output_clippedalignments_wig">
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212 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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213 </data>
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214 <data format="wig" label="${tool.name} weighted quality track on ${on_string}" name="output_weightedqual_wig">
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215 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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216 </data>
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217 <data format="wig" label="${tool.name} weighted MQ track on ${on_string}" name="output_weightedmq_wig">
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218 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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219 </data>
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220 <data format="wig" label="${tool.name} GC track on ${on_string}" name="output_gc_wig">
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221 <filter>options['selection_mode'] == 'advanced' and options['tracks']</filter>
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222 </data>
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223 </outputs>
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224 <tests>
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225 <test>
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226 <param name="reference_genome_source" value="history" />
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227 <param ftype="fasta" name="history_item" value="test1.fasta" />
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228 <param name="input_bams" value="test1.bam" />
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229 <param name="variant_calling" value="true" />
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230 <output file="test1.vcf" ftype="vcf" name="output_vcf" lines_diff="6" />
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231 <output file="test_output1.fasta" ftype="fasta" name="output_fasta" />
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232 </test>
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233 </tests>
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234 <help><![CDATA[
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235 Pilon is a software tool which can be used to:
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236
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237 * Automatically improve draft assemblies
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238
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239 * Find variation among strains, including large event detection
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240
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241 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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242
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243 * Single base differences
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244
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245 * Small indels
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246
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247 * Larger indel or block substitution events
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248
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249 * Gap filling
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250
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251 * Identification of local misassemblies, including optional opening of new gaps
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252
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253 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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254
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255 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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256
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257 Note on **mindepth**:
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258
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259 Variants (snps and indels) will only be called if there is coverage of good pairs
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260 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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261 fraction < 1, then minimum depth is computed by multiplying this value by the mean
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262 coverage for the region, with a minumum value of 5 (default 0.1: min depth to call
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263 is 10% of mean coverage or 5, whichever is greater).
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264
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265 Note on **stray read filtering**
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266
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267 By default a pass is made through the input BAM files to identify stray pairs, that is,
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268 those pairs in which both reads are aligned but not marked valid because they have
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269 inconsistent orientation or separation. Identifying stray pairs can help fill gaps
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270 and assemble larger insertions, especially of repeat content. However, doing so
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271 sometimes consumes considerable memory.
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272 ]]></help>
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273 <citations>
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274 <citation type="bibtex">@article{Walker_2014,
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275 title={Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement},
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276 volume={9}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0112963},
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277 DOI={10.1371/journal.pone.0112963}, number={11}, journal={PLoS ONE},
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278 publisher={Public Library of Science (PLoS)},
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279 author={Walker, Bruce J. and Abeel, Thomas and Shea, Terrance and
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280 Priest, Margaret and Abouelliel, Amr and Sakthikumar, Sharadha and Cuomo, Christina A. and
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281 Zeng, Qiandong and Wortman, Jennifer and Young, Sarah K. and et al.},
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282 editor={Wang, Junwen}, year={2014}, month={Nov}, pages={e112963}}</citation>
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283 </citations>
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284 </tool>