annotate tophat2/tophat2_wrapper.xml @ 30:dfbec245b12a draft

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author scottx611x
date Fri, 08 Jul 2016 11:50:18 -0400
parents 4e7fe3a94ed6
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1 <tool id="tophat2" name="TopHat" version="2.1.0">
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2 <!-- Wrapper compatible with Tophat version 2.0.0+ -->
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3 <description>Gapped-read mapper for RNA-seq data</description>
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4 <macros>
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5 <import>tophat_macros.xml</import>
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6 <xml name="paired_parameters">
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7 <param name="mate_inner_distance" type="integer" value="300" label="Mean Inner Distance between Mate Pairs" help="-r/--mate-inner-dist; This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 50bp."/>
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8 <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="--mate-std-dev; The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp."/>
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9 <!-- Discordant pairs. -->
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10 <param name="report_discordant_pairs" type="select" label="Report discordant pair alignments?" help="--no-discordant">
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11 <option value="No">No</option>
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12 <option selected="True" value="Yes">Yes</option>
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13 </param>
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14 </xml>
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15 <macro name="dbKeyActions">
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16 <actions>
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17 <conditional name="refGenomeSource.genomeSource">
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18 <when value="indexed">
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19 <action type="metadata" name="dbkey">
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20 <option type="from_data_table" name="tophat2_indexes" column="1" offset="0">
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21 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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22 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
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23 </option>
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24 </action>
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25 </when>
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26 <when value="history">
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27 <action type="metadata" name="dbkey">
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28 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
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29 </action>
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30 </when>
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31 </conditional>
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32 </actions>
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33 </macro>
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34 </macros>
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35 <requirements>
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36 <requirement type="package" version="2.2.5">bowtie2</requirement>
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37 <requirement type="package" version="2.1.0">tophat</requirement>
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38 </requirements>
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39 <stdio>
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40 <regex match="Exception|Error" source="both" level="fatal" description="Tool execution failed"/>
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41 <regex match=".*" source="both" level="log" description="tool progress"/>
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42 </stdio>
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43 <version_command>tophat2 --version</version_command>
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45 <command>
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46 ##
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47 ## Set path to index, building the reference if necessary.
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48 ##
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49
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50 #set index_path = ''
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51 #if $refGenomeSource.genomeSource == "history":
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52 bowtie2-build "$refGenomeSource.ownFile" genome ; ln -s "$refGenomeSource.ownFile" genome.fa ;
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53 #set index_path = 'genome'
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54 #else:
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55 #set index_path = $refGenomeSource.index.fields.path
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56 #end if
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57
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58 ##
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59 ## Run tophat.
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60 ##
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61
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62 tophat2
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63
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64 ## Change this to accommodate the number of threads you have available.
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65 --num-threads \${GALAXY_SLOTS:-4}
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66
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67 ## Set params.
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68 #if $params.settingsType == "full":
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69 --read-mismatches $params.read_mismatches
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70 #if str($params.bowtie_n) == "Yes":
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71 --bowtie-n
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72 #end if
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73
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74 --read-edit-dist $params.read_edit_dist
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75 --read-realign-edit-dist $params.read_realign_edit_dist
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76 -a $params.anchor_length
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77 -m $params.splice_mismatches
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78 -i $params.min_intron_length
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79 -I $params.max_intron_length
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80 -g $params.max_multihits
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81 --min-segment-intron $params.min_segment_intron
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82 --max-segment-intron $params.max_segment_intron
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83 --segment-mismatches $params.seg_mismatches
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84 --segment-length $params.seg_length
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85 --library-type $params.library_type
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86
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87 ## Indel search.
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88 #if $params.indel_search.allow_indel_search == "Yes":
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89 ## --allow-indels
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90 --max-insertion-length $params.indel_search.max_insertion_length
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91 --max-deletion-length $params.indel_search.max_deletion_length
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92 #else:
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93 --no-novel-indels
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94 #end if
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95
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96 ## Supplying junctions parameters.
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97 #if $params.own_junctions.use_junctions == "Yes":
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98 #if $params.own_junctions.gene_model_ann.use_annotations == "indexed"
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99 -G $params.own_junctions.gene_model_ann.gene_annotation_model.fields.path
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100 #elif $params.own_junctions.gene_model_ann.use_annotations == "history"
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101 -G $params.own_junctions.gene_model_ann.gene_annotation_model
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102 #end if
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103 #if $params.own_junctions.raw_juncs.use_juncs == "Yes":
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104 -j $params.own_junctions.raw_juncs.raw_juncs
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105 #end if
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106 #if str($params.own_junctions.no_novel_juncs) == "Yes":
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107 --no-novel-juncs
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108 #end if
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109 #end if
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110
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111 #if $params.coverage_search.use_search == "Yes":
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112 --coverage-search
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113 --min-coverage-intron $params.coverage_search.min_coverage_intron
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114 --max-coverage-intron $params.coverage_search.max_coverage_intron
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115 #else:
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116 --no-coverage-search
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117 #end if
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118
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119 #if str($params.microexon_search) == "Yes":
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120 --microexon-search
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121 #end if
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122
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123 #if $params.fusion_search.do_search == "Yes":
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124 --fusion-search
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125 --fusion-anchor-length $params.fusion_search.anchor_len
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126 --fusion-min-dist $params.fusion_search.min_dist
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127 --fusion-read-mismatches $params.fusion_search.read_mismatches
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128 --fusion-multireads $params.fusion_search.multireads
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129 --fusion-multipairs $params.fusion_search.multipairs
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130 --fusion-ignore-chromosomes "$params.fusion_search.ignore_chromosomes"
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131 #end if
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132
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133 #if $params.bowtie2_settings.b2_settings == "Yes":
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134 #if $params.bowtie2_settings.preset.b2_preset == "Yes":
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135 --b2-$params.bowtie2_settings.preset.b2_preset_select
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136 #end if
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137 #end if
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138
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139 #end if
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140
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141 ## Read group information.
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142 #if $readGroup.specReadGroup == "yes"
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143 --rg-id "$readGroup.rgid"
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144 --rg-library "$readGroup.rglb"
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145 --rg-platform "$readGroup.rgpl"
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146 --rg-sample "$readGroup.rgsm"
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147 #end if
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148
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149 ## Set index path, inputs and parameters specific to paired data.
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150 #if $singlePaired.sPaired != "single"
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151 -r $singlePaired.mate_inner_distance
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152 --mate-std-dev=$singlePaired.mate_std_dev
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153
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154 #if str($singlePaired.report_discordant_pairs) == "No":
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155 --no-discordant
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156 #end if
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157
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158 #if $singlePaired.sPaired == "paired"
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159 ${index_path} "$singlePaired.input1" "$singlePaired.input2"
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160 #else
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161 ${index_path} "$singlePaired.input.forward" "$singlePaired.input.reverse"
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162 #end if
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163 #else
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164 ${index_path} "$singlePaired.input1"
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165 #end if
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166 </command>
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167
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168 <inputs>
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169 <conditional name="singlePaired">
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170 <param name="sPaired" type="select" label="Is this single-end or paired-end data?">
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171 <option value="single">Single-end</option>
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172 <option value="paired">Paired-end (as individual datasets)</option>
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173 <option value="paired_collection">Paired-end (as collection)</option>
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174 </param>
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175 <when value="single">
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176 <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Must have Sanger-scaled quality values with ASCII offset 33"/>
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177 </when>
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178 <when value="paired">
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179 <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Must have Sanger-scaled quality values with ASCII offset 33" />
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180 <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Must have Sanger-scaled quality values with ASCII offset 33" />
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181 <expand macro="paired_parameters" />
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182 </when>
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183 <when value="paired_collection">
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184 <param format="fastqsanger" name="input" type="data_collection" collection_type="paired" label="RNA-Seq FASTQ paired reads" help="Must have Sanger-scaled quality values with ASCII offset 33" />
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185 <expand macro="paired_parameters" />
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186 </when>
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187 </conditional>
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188 <expand macro="refGenomeSourceConditional">
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189 <options from_data_table="tophat2_indexes">
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scottx611x
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190 <filter type="sort_by" column="2"/>
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scottx611x
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191 <validator type="no_options" message="No genomes are available for the selected input dataset"/>
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scottx611x
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192 </options>
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scottx611x
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193 </expand>
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scottx611x
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194 <conditional name="params">
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195 <param name="settingsType" type="select" label="TopHat settings to use" help="You can use the default settings or set custom values for any of Tophat's parameters.">
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196 <option value="preSet">Use Defaults</option>
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197 <option value="full">Full parameter list</option>
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198 </param>
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scottx611x
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199 <when value="preSet" />
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scottx611x
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200 <!-- Full/advanced params. -->
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201 <when value="full">
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202 <param name="read_realign_edit_dist" type="integer" value="1000" label="Max realign edit distance" help="--read-realign-edit-dist; Some of the reads spanning multiple exons may be mapped incorrectly as a contiguous alignment to the genome even though the correct alignment should be a spliced one - this can happen in the presence of processed pseudogenes that are rarely (if at all) transcribed or expressed. This option can direct TopHat to re-align reads for which the edit distance of an alignment obtained in a previous mapping step is above or equal to this option value. If you set this option to 0, TopHat will map every read in all the mapping steps (transcriptome if you provided gene annotations, genome, and finally splice variants detected by TopHat), reporting the best possible alignment found in any of these mapping steps. This may greatly increase the mapping accuracy at the expense of an increase in running time. The default value for this option is set such that TopHat will not try to realign reads already mapped in earlier steps." />
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203
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204 <param name="read_edit_dist" type="integer" value="2" label="Max edit distance" help="--read-edit-dist; Final read alignments having more than these many edit distance are discarded." />
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205
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206 <param name="library_type" type="select" label="Library Type" help="--library-type; TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.">
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207 <option value="fr-unstranded">FR Unstranded</option>
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208 <option value="fr-firststrand">FR First Strand</option>
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scottx611x
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209 <option value="fr-secondstrand">FR Second Strand</option>
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scottx611x
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210 </param>
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211 <param name="read_mismatches" type="integer" value="2" label="Final read mismatches" help="--read-mismatches; Final read alignments having more than these many mismatches are discarded." />
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212 <param name="bowtie_n" type="select" label="Use bowtie -n mode" help="--bowtie-n; TopHat uses &quot;-v&quot; in Bowtie for initial read mapping (the default), but with this option, &quot;-n&quot; is used instead. Read segments are always mapped using &quot;-v&quot; option.">
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213 <option selected="true" value="No">No</option>
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214 <option value="Yes">Yes</option>
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215 </param>
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216 <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="-a/--min-anchor-length; TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one read with this many bases on each side. This must be at least 3 and the default is 8." />
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217 <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" help="-m/--splice-mismatches; The default is 0."/>
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218 <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="-i/--min-intron-length; TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70." />
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219 <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="-I/--max-intron-length; When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000." />
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220
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221 <expand macro="indel_searchConditional" />
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scottx611x
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222
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223 <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" help="-g/--max-multihits; Instructs TopHat to allow up to this many alignments to the reference for a given read, and choose the alignments based on their alignment scores if there are more than this number. The default is 20 for read mapping. Unless you use --report-secondary-alignments, TopHat will report the alignments with the best alignment score. If there are more alignments with the same score than this number, TopHat will randomly report only this many alignments. In case of using --report-secondary-alignments, TopHat will try to report alignments up to this option value, and TopHat may randomly output some of the alignments with the same score to meet this number."/>
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224 <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" help="--min-segment-intron; The minimum intron length that may be found during split-segment search. The default is 50."/>
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225 <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" help="--max-segment-intron; The maximum intron length that may be found during split-segment search. The default is 500000."/>
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226 <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" help="--segment-mismatches; Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2."/>
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227 <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" help="--segment-length; Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25."/>
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228 <param name="output_unmapped" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output unmapped reads" help="If checked, a BAM with the unmapped reads will be added to the history" />
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229 <!-- Options for supplying own junctions. -->
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scottx611x
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230 <expand macro="own_junctionsConditional" />
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scottx611x
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231 <!-- Coverage search. -->
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scottx611x
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232 <conditional name="coverage_search">
23
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233 <param name="use_search" type="select" label="Use coverage-based search for junctions" help="Select 'Auto' to let TopHat decide when to enable coverage search (e.g. disable it for reads 75bp or longer). Select 'Yes' to enforce maximum sensitivity and to specify minimum and maximum intron length">
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234 <option selected="true" value="auto">Auto</option>
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235 <option value="No">No (--no-coverage-search)</option>
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diff changeset
236 <option value="Yes">Yes (--coverage-search)</option>
0
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237 </param>
23
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238 <when value="auto" />
0
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239 <when value="Yes">
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240 <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" help="--min-coverage-intron; The minimum intron length that may be found during coverage search. The default is 50."/>
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241 <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" help="--max-coverage-intron; The maximum intron length that may be found during coverage search. The default is 20000."/>
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242 </when>
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scottx611x
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243 <when value="No" />
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scottx611x
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244 </conditional>
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245
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246 <!-- Microexon search params -->
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247 <param name="microexon_search" type="select" label="Use Microexon Search" help="--microexon-search; With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
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248 <option value="No">No</option>
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249 <option value="Yes">Yes</option>
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250 </param>
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251
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252 <!-- Fusion mapping. -->
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253 <conditional name="fusion_search">
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254 <param name="do_search" type="select" label="Do Fusion Search" help="Reads can be aligned to potential fusion transcripts if the --fusion-search option is specified. The fusion alignments are reported in SAM format using custom fields XF and XP (see the output format) and some additional information about fusions will be reported (see fusions.out). Once mapping is done, you can run tophat-fusion-post to filter out fusion transcripts (see the TopHat-Fusion website for more details).">
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255 <option selected="true" value="No">No</option>
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256 <option value="Yes">Yes</option>
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scottx611x
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257 </param>
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scottx611x
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258 <when value="No" />
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scottx611x
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259 <when value="Yes">
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260 <param name="anchor_len" type="integer" value="20" label="Anchor Length" help="--fusion-anchor-length; A 'supporting' read must map to both sides of a fusion by at least this many bases. The default is 20."/>
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261 <param name="min_dist" type="integer" value="10000000" label="Minimum Distance" help="--fusion-min-dist; For intra-chromosomal fusions, TopHat-Fusion tries to find fusions separated by at least this distance. The default is 10000000."/>
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262 <param name="read_mismatches" type="integer" value="2" label="Read Mismatches" help="--fusion-read-mismatches; Reads support fusions if they map across fusion with at most this many mismatches. The default is 2."/>
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263 <param name="multireads" type="integer" value="2" label="Multireads" help="--fusion-multireads; Reads that map to more than this many places will be ignored. It may be possible that a fusion is supported by reads (or pairs) that map to multiple places. The default is 2."/>
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264 <param name="multipairs" type="integer" value="2" label="Multipairs" help="--fusion-multipairs; Pairs that map to more than this many places will be ignored. The default is 2."/>
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265 <param name="ignore_chromosomes" type="text" value='' label="--fusion-ignore-chromosomes; Ignore some chromosomes such as chrM when detecting fusion break points"/>
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266 </when>
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267 </conditional>
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268
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269 <!-- Bowtie2 settings. -->
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270 <conditional name="bowtie2_settings">
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271 <param name="b2_settings" type="select" label="Set Bowtie2 settings">
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272 <option selected="true" value="No">No</option>
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273 <option value="Yes">Yes</option>
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scottx611x
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274 </param>
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scottx611x
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275 <when value="No" />
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276 <when value="Yes">
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scottx611x
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277 <conditional name="preset">
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278 <param name="b2_preset" type="select" label="Use Preset options">
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279 <option selected="true" value="Yes">Yes</option>
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280 <option value="No">No</option>
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scottx611x
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281 </param>
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282 <when value="Yes">
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283 <param name="b2_preset_select" type="select" label="Preset option">
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284 <option value="very-fast">Very fast</option>
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285 <option value="fast">Fast</option>
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286 <option selected="true" value="sensitive">Sensitive</option>
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287 <option value="very-sensitive">Very sensitive</option>
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scottx611x
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288 </param>
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289 </when>
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scottx611x
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290 <!-- TODO: -->
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291 <when value="No" />
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292 </conditional>
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293 </when>
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294 </conditional>
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295 </when> <!-- full -->
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296 </conditional> <!-- params -->
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297 <conditional name="readGroup">
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298 <param name="specReadGroup" type="select" label="Specify read group?">
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299 <option value="yes">Yes</option>
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scottx611x
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300 <option value="no" selected="True">No</option>
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scottx611x
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301 </param>
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302 <when value="yes">
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303 <param name="rgid" type="text" label="Read group identifier (ID). Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group IDs may be modified when merging SAM files in order to handle collisions." />
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304 <param name="rglb" type="text" label="Library name (LB)" help="Required if RG specified" />
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305 <param name="rgpl" type="text" label="Platform/technology used to produce the reads (PL)" help="Required if RG specified. Valid values : CAPILLARY, LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO" />
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306 <param name="rgsm" type="text" label="Sample (SM)" help="Required if RG specified. Use pool name where a pool is being sequenced" />
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307 </when>
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308 <when value="no" />
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309 </conditional> <!-- readGroup -->
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310 </inputs>
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311
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312 <outputs>
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313 <data format="txt" name="align_summary" label="${tool.name} on ${on_string}: align_summary" from_work_dir="tophat_out/align_summary.txt"/>
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314 <data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out">
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315 <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter>
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316 </data>
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317 <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
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318 <expand macro="dbKeyActions" />
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319 </data>
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320 <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
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scottx611x
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321 <expand macro="dbKeyActions" />
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322 </data>
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323 <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed">
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324 <expand macro="dbKeyActions" />
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325 </data>
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326 <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam">
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scottx611x
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327 <expand macro="dbKeyActions" />
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328 </data>
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329 <data format="bam" name="unmapped" label="${tool.name} on ${on_string}: unmapped" from_work_dir="tophat_out/unmapped.bam">
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330 <filter>(params['settingsType'] == 'full' and params['output_unmapped'])</filter>
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331 <expand macro="dbKeyActions" />
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332 </data>
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333
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334 </outputs>
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335
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336 <tests>
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337 <!-- Test base-space single-end reads with pre-built index and preset parameters -->
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scottx611x
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338 <test>
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scottx611x
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339 <!-- TopHat commands:
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scottx611x
parents:
diff changeset
340 tophat2 -o tmp_dir -p 1 tophat_in1 test-data/tophat_in2.fastqsanger
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
341 Rename the files in tmp_dir appropriately
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
342 -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
343 <param name="sPaired" value="single" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
344 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
345 <param name="genomeSource" value="indexed" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
346 <param name="index" value="tophat_test" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
347 <param name="settingsType" value="preSet" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
348 <param name="specReadGroup" value="no" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
349 <output name="junctions" file="tophat2_out1j.bed" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
350 <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
351 </test>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
352 <!-- Test using base-space test data: paired-end reads, index from history. -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
353 <test>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
354 <!-- TopHat commands:
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
355 bowtie2-build -f test-data/tophat_in1.fasta tophat_in1
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
356 tophat2 -o tmp_dir -p 1 -r 20 tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
357 Rename the files in tmp_dir appropriately
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
358 -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
359 <param name="sPaired" value="paired" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
360 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
361 <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
362 <param name="genomeSource" value="history" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
363 <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
364 <param name="mate_inner_distance" value="20" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
365 <param name="settingsType" value="preSet" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
366 <param name="specReadGroup" value="no" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
367 <output name="junctions" file="tophat2_out2j.bed" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
368 <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
369 </test>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
370 <test>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
371 <!-- Same test as above but with a collection. -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
372 <param name="sPaired" value="paired_collection" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
373 <param name="input">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
374 <collection type="paired">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
375 <element name="forward" value="tophat_in2.fastqsanger" ftype="fastqsanger" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
376 <element name="reverse" value="tophat_in3.fastqsanger" ftype="fastqsanger" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
377 </collection>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
378 </param>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
379 <param name="genomeSource" value="history" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
380 <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
381 <param name="mate_inner_distance" value="20" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
382 <param name="settingsType" value="preSet" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
383 <param name="specReadGroup" value="no" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
384 <output name="junctions" file="tophat2_out2j.bed" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
385 <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
386 </test>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
387 <!-- Test base-space single-end reads with user-supplied reference fasta and full parameters -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
388 <test>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
389 <!-- TopHat commands:
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
390 bowtie2-build -f test-data/tophat_in1.fasta tophat_in1
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
391 tophat2 -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
392 Replace the + with double-dash
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
393 Rename the files in tmp_dir appropriately
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
394 -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
395 <conditional name="singlePaired">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
396 <param name="sPaired" value="single"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
397 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
398 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
399 <param name="genomeSource" value="history"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
400 <param name="ownFile" value="tophat_in1.fasta"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
401 <conditional name="params">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
402 <param name="settingsType" value="full"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
403 <param name="library_type" value="FR Unstranded"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
404 <param name="read_mismatches" value="2"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
405 <param name="bowtie_n" value="No"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
406 <param name="anchor_length" value="8"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
407 <param name="splice_mismatches" value="0"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
408 <param name="min_intron_length" value="70"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
409 <param name="max_intron_length" value="500000"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
410 <param name="max_multihits" value="40"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
411 <param name="min_segment_intron" value="50" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
412 <param name="max_segment_intron" value="500000" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
413 <param name="seg_mismatches" value="2"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
414 <param name="seg_length" value="25"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
415 <conditional name="indel_search">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
416 <param name="allow_indel_search" value="Yes"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
417 <param name="max_insertion_length" value="3"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
418 <param name="max_deletion_length" value="3"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
419 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
420 <conditional name="own_junctions">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
421 <param name="use_junctions" value="Yes" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
422 <conditional name="gene_model_ann">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
423 <param name="use_annotations" value="No" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
424 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
425 <conditional name="raw_juncs">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
426 <param name="use_juncs" value="No" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
427 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
428 <conditional name="no_novel_juncs">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
429 <param name="no_novel_juncs" value="No" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
430 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
431 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
432 <conditional name="coverage_search">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
433 <param name="use_search" value="Yes" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
434 <param name="min_coverage_intron" value="50" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
435 <param name="max_coverage_intron" value="20000" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
436 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
437 <param name="microexon_search" value="Yes" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
438 <conditional name="bowtie2_settings">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
439 <param name="b2_settings" value="No" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
440 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
441 <!-- Fusion search params -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
442 <conditional name="fusion_search">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
443 <param name="do_search" value="Yes" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
444 <param name="anchor_len" value="21" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
445 <param name="min_dist" value="10000021" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
446 <param name="read_mismatches" value="3" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
447 <param name="multireads" value="4" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
448 <param name="multipairs" value="5" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
449 <param name="ignore_chromosomes" value="chrM"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
450 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
451 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
452 <conditional name="readGroup">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
453 <param name="specReadGroup" value="no" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
454 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
455 <output name="insertions" file="tophat_out3i.bed" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
456 <output name="deletions" file="tophat_out3d.bed" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
457 <output name="junctions" file="tophat2_out3j.bed" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
458 <output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
459 </test>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
460 <!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
461 <test>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
462 <!-- TopHat commands:
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
463 tophat2 -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search +report_discordant_pairs tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
464 Replace the + with double-dash
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
465 Rename the files in tmp_dir appropriately
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
466 -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
467 <conditional name="singlePaired">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
468 <param name="sPaired" value="paired"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
469 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
470 <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
471 <param name="mate_inner_distance" value="20"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
472 <param name="report_discordant_pairs" value="Yes" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
473 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
474 <param name="genomeSource" value="indexed"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
475 <param name="index" value="tophat_test"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
476 <conditional name="params">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
477 <param name="settingsType" value="full"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
478 <param name="library_type" value="FR Unstranded"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
479 <param name="read_mismatches" value="5"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
480 <!-- Error: the read mismatches (5) and the read gap length (2) should be less than or equal to the read edit dist (2) -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
481 <param name="read_edit_dist" value="5" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
482 <param name="bowtie_n" value="Yes"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
483 <param name="mate_std_dev" value="20"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
484 <param name="anchor_length" value="8"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
485 <param name="splice_mismatches" value="0"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
486 <param name="min_intron_length" value="70"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
487 <param name="max_intron_length" value="500000"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
488 <param name="max_multihits" value="40"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
489 <param name="min_segment_intron" value="50" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
490 <param name="max_segment_intron" value="500000" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
491 <param name="seg_mismatches" value="2"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
492 <param name="seg_length" value="25"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
493 <conditional name="indel_search">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
494 <param name="allow_indel_search" value="No"/>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
495 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
496 <conditional name="own_junctions">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
497 <param name="use_junctions" value="Yes" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
498 <conditional name="gene_model_ann">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
499 <param name="use_annotations" value="No" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
500 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
501 <conditional name="raw_juncs">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
502 <param name="use_juncs" value="No" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
503 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
504 <conditional name="no_novel_juncs">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
505 <param name="no_novel_juncs" value="No" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
506 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
507 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
508 <conditional name="coverage_search">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
509 <param name="use_search" value="No" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
510 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
511 <param name="microexon_search" value="Yes" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
512 <conditional name="bowtie2_settings">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
513 <param name="b2_settings" value="No" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
514 </conditional>
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
515 <!-- Fusion search params -->
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
516 <conditional name="fusion_search">
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
517 <param name="do_search" value="Yes" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
518 <param name="anchor_len" value="21" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
519 <param name="min_dist" value="10000021" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
520 <param name="read_mismatches" value="3" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
521 <param name="multireads" value="4" />
620cb7a7ef60 Uploaded
scottx611x
parents:
diff changeset
522 <param name="multipairs" value="5" />
620cb7a7ef60 Uploaded
scottx611x
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523 <param name="ignore_chromosomes" value="chrM"/>
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524 </conditional>
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525 </conditional>
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526 <conditional name="readGroup">
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527 <param name="specReadGroup" value="no" />
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528 </conditional>
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529 <output name="junctions" file="tophat2_out4j.bed" />
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530 <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" />
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531 </test>
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532 </tests>
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533 <help>
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534 **TopHat Overview**
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535
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536 TopHat_ is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie(2), and then analyzes the mapping results to identify splice junctions between exons.
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537
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538 .. _TopHat: http://ccb.jhu.edu/software/tophat/
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539
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540 ------
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541
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542 **Know what you are doing**
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543
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544 .. class:: warningmark
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545
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546 There is no such thing (yet) as an automated gearshift in splice junction identification. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
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547
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548 .. __: http://ccb.jhu.edu/software/tophat/manual.shtml
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549
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550 ------
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551
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552 **Input formats**
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553
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554 TopHat accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
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555
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556 ------
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557
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558 **Outputs**
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559
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560 TopHat produces two output files:
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561
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562 - junctions -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.
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563 - accepted_hits -- A list of read alignments in BAM_ format.
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564
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565 .. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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566 .. _BAM: http://samtools.sourceforge.net/
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567
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568 Two other possible outputs, depending on the options you choose, are insertions and deletions, both of which are in BED format.
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569
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570 -------
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571
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572 **TopHat settings**
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573
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574 All of the options have a default value. You can change any of them. Some of the options in TopHat have been implemented here.
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575
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576 ------
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577
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578 **TopHat parameter list**
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579
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580 This is a list of implemented TopHat options::
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581
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582 -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments
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583 selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter
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584 is required for paired end runs.
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585 --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.
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586 -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced
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587 alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one
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588 read with this many bases on each side. This must be at least 3 and the default is 8.
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589 -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0.
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590 -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70.
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591 -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000.
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592 -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many
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593 alignments. The default is 40.
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594 -G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.
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595 -j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.
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596 -no-novel-juncs Only look for junctions indicated in the supplied GFF file. (ignored without -G)
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597 --no-coverage-search Disables the coverage based search for junctions.
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598 --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.
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599 --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.
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600 --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2.
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601 --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.
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602 --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50.
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603 --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000.
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604 --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50.
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605 --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000.
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606 </help>
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607 <citations>
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608 <citation type="doi">10.1186/gb-2013-14-4-r36</citation>
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609 </citations>
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610 </tool>