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0
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1 <tool id="gsnap" name="GSNAP" version="2.0.1">
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2 <description>Genomic Short-read Nucleotide Alignment Program</description>
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3 <requirements>
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1
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4 <requirement type="package" version="2011-11-30">gmap</requirement>
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0
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5 </requirements>
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6 <version_string>gsnap --version</version_string>
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7 <command>
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8 #import os.path, re
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9 gsnap
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10 --nthreads="4" --ordered
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11 #if $refGenomeSource.genomeSource == "gmapdb":
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12 #set $gmapdb = $os.listdir($refGenomeSource.gmapdb.extra_files_path)[0]
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13 --dir=$refGenomeSource.gmapdb.extra_files_path --db=$refGenomeSource.gmapdb.metadata.db_name
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14 #else:
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15 --dir=$os.path.dirname($refGenomeSource.gmapindex.value) --db=$os.path.basename($refGenomeSource.gmapindex.value)
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16 #end if
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17 #if $refGenomeSource.kmer != None and len($refGenomeSource.kmer.__str__) == 2:
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18 --kmer=$refGenomeSource.kmer
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19 #end if
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20 #if $refGenomeSource.use_splicing.src == 'gmapdb':
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21 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:
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22 -s $refGenomeSource.use_splicing.splicemap.value
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23 #if $computation.trim_mismatch_score.__str__ == '0':
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24 $ambig_splice_noclip
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25 #end if
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26 #end if
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27 #elif $refGenomeSource.use_splicing.src == 'history':
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28 #if $refGenomeSource.use_splicing.splicemap != None and len($refGenomeSource.use_splicing.splicemap.__str__) > 0:
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29 -S $os.path.dirname($refGenomeSource.use_splicing.splicemap) -s $os.path.basename($refGenomeSource.use_splicing.splicemap)
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30 #if $computation.trim_mismatch_score.__str__ == '0':
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31 $ambig_splice_noclip
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32 #end if
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33 #end if
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34 #end if
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35 #if $refGenomeSource.use_snps.src == 'gmapdb':
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36 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0:
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37 -v $refGenomeSource.use_snps.snpindex.value
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38 #end if
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39 #elif $refGenomeSource.use_snps.src == 'history':
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40 #if $refGenomeSource.use_snps.snpindex != None and len($refGenomeSource.use_snps.snpindex.__str__) > 0:
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41 -V $refGenomeSource.use_snps.snpindex.extra_files_path -v $refGenomeSource.use_snps.snpindex.metadata.snps_name
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42 #end if
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43 #end if
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44 #if $refGenomeSource.mode.__str__ != '':
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45 --mode=$refGenomeSource.mode
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46 #end if
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47 #* ## No longer in options as of version 2011-11-30
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48 #if $mapq_unique_score.__str__ != '':
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49 --mapq-unique-score=$mapq_unique_score
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50 #end if
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51 *#
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52 #if $computation.options == "advanced":
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53 #if $computation.max_mismatches.__str__ != '':
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54 --max-mismatches=$computation.max_mismatches
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55 #end if
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56 $computation.query_unk_mismatch
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57 $computation.genome_unk_mismatch
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58 #if $computation.terminal_threshold.__str__ != '':
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59 --terminal-threshold=$computation.terminal_threshold
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60 #end if
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61 #if $computation.indel_penalty.__str__ != '':
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62 --indel-penalty=$computation.indel_penalty
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63 #end if
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64 #if $computation.indel_endlength.__str__ != '':
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65 --indel-endlength=$computation.indel_endlength
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66 #end if
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67 #if $computation.max_middle_insertions.__str__ != '':
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68 --max-middle-insertions=$computation.max_middle_insertions
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69 #end if
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70 #if $computation.max_middle_deletions.__str__ != '':
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71 --max-middle-deletions=$computation.max_middle_deletions
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72 #end if
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73 #if $computation.max_end_insertions.__str__ != '':
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74 --max-end-insertions=$computation.max_end_insertions
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75 #end if
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76 #if $computation.max_end_deletions.__str__ != '':
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77 --max-end-deletions=$computation.max_end_deletions
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78 #end if
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79 #if $computation.suboptimal_levels.__str__ != '':
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80 --suboptimal-levels=$computation.suboptimal_levels
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81 #end if
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82 #if $computation.adapter_strip.__str__ != '':
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83 --adapter-strip=$computation.adapter_strip
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84 #end if
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85 #if $computation.trim_mismatch_score.__str__ != '':
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86 --trim-mismatch-score=$computation.trim_mismatch_score
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87 #end if
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88 #if $computation.trim_indel_score.__str__ != '':
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89 --trim-indel-score=$computation.trim_indel_score
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90 #end if
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91 ## TODO - do we need these options (Is it tally XOR runlength?):
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92 ## --tallydir= --use-tally=tally
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93 ## --runlengthdir --use-runlength=runlength
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94 #if $computation.use_tally != None and len($computation.use_tally.__str__) > 0:
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95 ##--tallydir $os.path.dirname($computation.use_tally) --use-tally $os.path.basename($computation.use_tally)
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96 --use-tally=$computation.use_tally
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97 #end if
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98 ## gmap options
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99 #if $computation.gmap_mode.__str__ != '' and $computation.gmap_mode.__str__ != 'None':
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100 --gmap-mode='$computation.gmap_mode'
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101 #end if
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102 #if $computation.trigger_score_for_gmap.__str__ != '':
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103 --trigger-score-for-gmap=$computation.trigger_score_for_gmap
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104 #end if
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105 #if $computation.max_gmap_pairsearch.__str__ != '' and $re.search("pairsearch",$computation.gmap_mode):
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106 --max-gmap-pairsearch=$computation.max_gmap_pairsearch
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107 #end if
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108 #if $computation.max_gmap_terminal.__str__ != '' and $re.search("terminal",$computation.gmap_mode):
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109 --max-gmap-terminal=$computation.max_gmap_terminal
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110 #end if
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111 #if $computation.max_gmap_improvement.__str__ != '' and $re.search("improv",$computation.gmap_mode):
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112 --max-gmap-improvement=$computation.max_gmap_improvement
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113 #end if
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114 #if $computation.microexon_spliceprob.__str__ != '':
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115 --microexon-spliceprob=$computation.microexon_spliceprob
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116 #end if
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117 #end if
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118 #if $splicing.options == "advanced":
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119 $splicing.novelsplicing
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120 #if $splicing.localsplicedist.__str__ != '':
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121 --localsplicedist=$splicing.localsplicedist
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122 #end if
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123 #if $splicing.local_splice_penalty.__str__ != '':
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124 --local-splice-penalty=$splicing.local_splice_penalty
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125 #end if
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126 #if $splicing.distant_splice_penalty.__str__ != '':
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127 --distant-splice-penalty=$splicing.distant_splice_penalty
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128 #end if
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129 #if $splicing.local_splice_endlength.__str__ != '':
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130 --local-splice-endlength=$splicing.local_splice_endlength
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131 #end if
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132 #if $splicing.distant_splice_endlength.__str__ != '':
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133 --distant-splice-endlength=$splicing.distant_splice_endlength
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134 #end if
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135 #if $splicing.distant_splice_identity.__str__ != '':
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136 --distant-splice-identity=$splicing.distant_splice_identity
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137 #end if
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138 #end if
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139 #if $output.options == "advanced":
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140 #if $output.npath.__str__ != '':
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141 --npath=$output.npath
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142 #end if
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143 $output.quiet_if_excessive
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144 $output.show_refdiff
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145 $output.clip_overlap
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146 #end if
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147 #if $result.format == "sam":
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148 --format=sam
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149 $result.no_sam_headers
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150 #if $result.read_group_id.__str__.strip != '':
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151 --read-group-id='$result.read_group_id'
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152 #end if
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153 #if $result.read_group_name.__str__ != '':
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154 --read-group-name='$result.read_group_name'
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155 #end if
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156 #if $result.read_group_library.__str__ != '':
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157 --read-group-library='$result.read_group_library'
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158 #end if
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159 #if $result.read_group_platform.__str__ != '':
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160 --read-group-platform='$result.read_group_platform'
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161 #end if
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162 #if $result.quality_shift.__str__ != '':
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163 --quality-shift=$result.quality_shift
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164 #end if
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165 #elif $result.format == "goby":
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166 #if $result.goby_output.__str__ != '':
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167 --goby-output='$result.goby_output'
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168 #end if
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169 #if $result.creads_window_start.__str__ != '':
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170 --creads-window-start=$result.creads_window_start
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171 #end if
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172 #if $result.creads_window_end.__str__ != '':
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173 --creads-window-end=$result.creads_window_end
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174 #end if
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175 $result.creads_complement
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176 #end if
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177 #if $results.split_output == 'yes':
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178 --split-output=gsnap_out
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179 #if $results.fails.choice == 'nofails':
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180 --nofails
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181 #elif $results.fails.choice == 'failsonly':
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182 --failsonly
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183 #end if
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184 $results.fails_as_input
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185 #else
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186 #if $results.fails.choice == 'nofails':
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187 --nofails
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188 #elif $results.fails.choice == 'failsonly':
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189 --failsonly
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190 $results.fails.fails_as_input
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191 #end if
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192 #end if
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193 #if $seq.format == "gsnap_fasta":
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194 $seq.circularinput $seq.gsnap
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195 #else if $seq.format == "fastq":
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196 #if $seq.barcode_length.__str__ != '':
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197 --barcode-length=$seq.barcode_length
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198 #end if
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199 #if $seq.fastq_id_start.__str__ != '':
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200 --fastq-id-start=$seq.fastq_id_start
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201 #end if
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202 #if $seq.fastq_id_end.__str__ != '':
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203 --fastq-id-end=$seq.fastq_id_end
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204 #end if
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205 #if $seq.filter_chastity.__str__ != 'off':
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206 --filter-chastity=$seq.filter_chastity
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207 #end if
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208 #if $seq.paired.ispaired.__str__ == 'yes':
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209 #if $seq.paired.pairmax_dna.__str__ != '':
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210 --pairmax-dna=$seq.paired.pairmax_dna
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211 #end if
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212 #if $seq.paired.pairmax_rna.__str__ != '':
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213 --pairmax-rna=$seq.paired.pairmax_rna
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214 #end if
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215 #if $seq.paired.pairexpect.__str__ != '':
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216 --pairexpect=$seq.paired.pairexpect
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217 #end if
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218 #if $seq.paired.pairdev.__str__ != '':
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219 --pairdev=$seq.paired.pairdev
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220 #end if
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221 $seq.fastq $seq.paired.fastq
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222 #else
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223 $seq.fastq
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224 #end if
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225 #end if
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226 #if $results.split_output == 'yes':
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227 2> $gsnap_stderr
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228 #else:
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229 #if $results.fails.choice.__str__ == 'failsonly' and $results.fails.fails_as_input.__str__ != '':
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230 2> $gsnap_stderr > $gsnap_fq
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231 #else
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232 2> $gsnap_stderr > $gsnap_out
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233 #end if
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234 #end if
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235
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236 </command>
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237 <inputs>
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238 <!-- Input data -->
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239 <conditional name="seq">
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240 <param name="format" type="select" label="<H2>Input Sequences</H2>Select the input format" help="">
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241 <option value="fastq">Fastq</option>
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242 <!--
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243 <option value="goby">Goby compact-reads</option>
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244 -->
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245 <option value="gsnap_fasta">GNSAP fasta</option>
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246 </param>
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247 <when value="fastq">
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248 <param name="fastq" type="data" format="fastq" label="Select a fastq dataset" />
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249 <conditional name="paired">
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250 <param name="ispaired" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Use Paired Reads?"/>
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251 <when value="no"/>
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252 <when value="yes">
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253 <param name="fastq" type="data" format="fastq" label="Select the paired reads reverse dataset" />
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254 <param name="orientation" type="select" label="Orientation of paired-end reads" help="">
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255 <option value="FR">fwd-rev, typical Illumina default</option>
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256 <option value="RF">rev-fwd, for circularized inserts</option>
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257 <option value="FF">fwd-fwd, same strand</option>
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258 </param>
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259 <param name="pairmax_dna" type="integer" value="" optional="true" label="Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 1000)." help="Used if no splice file is provided and novelsplicing is off."/>
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260 <param name="pairmax_rna" type="integer" value="" optional="true" label="Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice (default 200000)." help="Used when novel splicing is specified or a splice file is provided. Should probably match the value for localsplicedist."/>
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261 <param name="pairexpect" type="integer" value="" optional="true" label="Expected paired-end length"
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262 help="Used for calling splices in medial part of paired-end reads (default 200)"/>
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263 <param name="pairdev" type="integer" value="" optional="true" label="Allowable deviation from expected paired-end length"
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264 help="Used for calling splices in medial part of paired-end reads (default 25)"/>
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265 </when>
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266 </conditional>
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267 <param name="barcode_length" type="integer" value="" optional="true" label="Amount of barcode to remove from start of read (default 0)" />
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268 <param name="fastq_id_start" type="integer" value="" optional="true" label="Starting field of identifier in FASTQ header, whitespace-delimited, starting from 1" />
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269 <param name="fastq_id_end" type="integer" value="" optional="true" label="Ending field of identifier in FASTQ header, whitespace-delimited, starting from 1"
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270 help="Examples:
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271 <br>@HWUSI-EAS100R:6:73:941:1973#0/1
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272 <br> . start=1, end=1 (default) => identifier is HWUSI-EAS100R:6:73:941:1973#0/1
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273 <br>@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
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274 <br> . start=1, end=1 => identifier is SRR001666.1
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275 <br> . start=2, end=2 => identifier is 071112_SLXA-EAS1_s_7:5:1:817:345
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276 <br> . start=1, end=2 => identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345"
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277 />
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278 <param name="filter_chastity" type="select" label="Skip reads marked by the Illumina chastity program"
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279 help="String after the accession having a 'Y' after the first colon, like this:
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280 <br>@accession 1:Y:0:CTTGTA
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281 <br>where the 'Y' signifies filtering by chastity.
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282 <br> For 'either', a 'Y' on either end of a paired-end read will be filtered.
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283 <br> For 'both', a 'Y' is required on both ends of a paired-end read (or on the only end of a single-end read)"
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284 >
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285 <option value="off">off - no filtering</option>
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286 <option value="either">either - a 'Y' on either end of a paired-end read</option>
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287 <option value="both">both - a 'Y' is required on both ends of a paired-end read or the only end of a single-end read</option>
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288 </param>
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289 </when>
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290 <!--
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291 <when value="goby">
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292 </when>
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293 -->
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294 <when value="gsnap_fasta">
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295 <param name="gsnap" type="data" format="fasta" label="Select a single-end dataset" help="GSNAP fasta must have the sequence entirely on one line, a second line is interpreted as the paired-end sequence"/>
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296 <param name="circularinput" type="boolean" checked="false" truevalue="--circular-input=true" falsevalue="" label="Circular-end data (paired reads are on same strand)"/>
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297 </when>
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298
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299 </conditional>
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300 <!-- No longer in options as of version 2011-11-30
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301 <param name="mapq_unique_score" type="integer" value="" optional="true" label="MAPQ score threshold"
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302 help="For multiple results, consider as a unique result if only one of the results has a MAPQ score equal or greater than this
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303 (if not selected, then reports all multiple results, up to npaths)" />
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304 -->
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305
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306 <!-- GMAPDB for alignment -->
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307 <conditional name="refGenomeSource">
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308 <param name="genomeSource" type="select" label="<HR><H2>Align To</H2>Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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309 <option value="indexed">Use a built-in index</option>
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310 <option value="gmapdb">Use a gmapdb from your history</option>
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311 </param>
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312 <when value="indexed">
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313 <param name="gmapindex" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
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314 <options from_file="gmap_indices.loc">
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315 <column name="uid" index="0" />
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316 <column name="dbkey" index="1" />
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|
|
317 <column name="name" index="2" />
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|
|
318 <column name="kmers" index="3" />
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|
|
319 <column name="maps" index="4" />
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|
320 <column name="snps" index="5" />
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|
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321 <column name="value" index="6" />
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|
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322 </options>
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323 </param>
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324
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325 <param name="kmer" type="select" data_ref="gmapindex" label="kmer size" help="Defaults to highest available kmer size">
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|
326 <options from_file="gmap_indices.loc">
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327 <column name="name" index="3"/>
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328 <column name="value" index="3"/>
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|
|
329 <filter type="param_value" ref="gmapindex" column="6"/>
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330 <filter type="multiple_splitter" column="3" separator=","/>
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331 <filter type="add_value" name="" value=""/>
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332 <filter type="sort_by" column="3"/>
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|
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333 </options>
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|
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334 </param>
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335
|
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336 <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase.">
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|
|
337 <option value="">standard</option>
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|
|
338 <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
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|
|
339 <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
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|
|
340 <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option>
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|
|
341 <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option>
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|
|
342 </param>
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343
|
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|
344 <conditional name="use_splicing">
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|
345 <param name="src" type="select" label="<HR>Known Splicesite and Introns"
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|
346 help="Look for splicing involving known sites or known introns at short or long distances
|
|
|
347 See README instructions for the distinction between known sites and known introns">
|
|
|
348 <option value="none" selected="true">None</option>
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|
349 <option value="gmapdb">From the GMAP Database</option>
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350 <option value="history">A Map in your history</option>
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|
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351 </param>
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|
|
352 <when value="none"/>
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353 <when value="history">
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354 <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map"
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355 help="built with GMAP IIT"/>
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356 </when>
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357 <when value="gmapdb">
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|
358 <param name="splicemap" type="select" data_ref="gmapindex" label="Use map for splicing involving known sites or known introns" help="">
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|
|
359 <options from_file="gmap_indices.loc">
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|
|
360 <column name="name" index="4"/>
|
|
|
361 <column name="value" index="4"/>
|
|
|
362 <filter type="param_value" ref="gmapindex" column="6"/>
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|
|
363 <filter type="multiple_splitter" column="4" separator=","/>
|
|
|
364 <filter type="add_value" name="" value=""/>
|
|
|
365 <filter type="sort_by" column="4"/>
|
|
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366 </options>
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|
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367 </param>
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|
|
368 </when>
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|
|
369 </conditional>
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|
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370
|
|
|
371 <conditional name="use_snps">
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|
|
372 <param name="src" type="select" label="<HR>Known SNPs" help="for SNP tolerant alignments">
|
|
|
373 <option value="none" selected="true">None</option>
|
|
|
374 <option value="gmapdb">From the GMAP Database</option>
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|
|
375 <option value="history">A SNP Index in your history</option>
|
|
|
376 </param>
|
|
|
377 <when value="none"/>
|
|
|
378 <when value="history">
|
|
|
379 <param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex"
|
|
|
380 help="built with GMAP SNP Index"/>
|
|
|
381 </when>
|
|
|
382 <when value="gmapdb">
|
|
|
383 <param name="snpindex" type="select" data_ref="gmapindex" label="Use database containing known SNPs" help="">
|
|
|
384 <options from_file="gmap_indices.loc">
|
|
|
385 <column name="name" index="5"/>
|
|
|
386 <column name="value" index="5"/>
|
|
|
387 <filter type="param_value" ref="gmapindex" column="6"/>
|
|
|
388 <filter type="multiple_splitter" column="5" separator=","/>
|
|
|
389 <filter type="add_value" name="" value=""/>
|
|
|
390 <filter type="sort_by" column="5"/>
|
|
|
391 </options>
|
|
|
392 </param>
|
|
|
393 </when>
|
|
|
394 </conditional>
|
|
|
395
|
|
|
396 </when>
|
|
|
397 <when value="gmapdb">
|
|
|
398 <param name="gmapdb" type="data" format="gmapdb" metadata_name="dbkey" label="Select a gmapdb"
|
|
|
399 help="A GMAP database built with GMAP Build"/>
|
|
|
400 <param name="kmer" type="select" data_ref="gmapdb" label="kmer size" help="Defaults to highest available kmer size">
|
|
|
401 <options>
|
|
|
402 <filter type="data_meta" ref="gmapdb" key="kmers" multiple="True" separator=","/>
|
|
|
403 </options>
|
|
|
404 </param>
|
|
|
405
|
|
|
406 <param name="mode" type="select" label="Alignment mode" help="Assumes cmetindex and atoiindex were run on the gmap datatbase.">
|
|
|
407 <option value="">standard</option>
|
|
|
408 <option value="cmet-stranded">cmet-stranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
|
|
|
409 <option value="cmet-nonstranded">cmet-nonstranded for bisulfite-treated DNA reads (tolerance to C-to-T changes)</option>
|
|
|
410 <option value="atoi-stranded">atoi-stranded for RNA-editing tolerance (A-to-G changes)</option>
|
|
|
411 <option value="atoi-nonstranded">atoi-nonstranded for RNA-editing tolerance (A-to-G changes)</option>
|
|
|
412 </param>
|
|
|
413
|
|
|
414 <conditional name="use_splicing">
|
|
|
415 <param name="src" type="select" label="<HR>Known Splicesite and Introns"
|
|
|
416 help="Look for splicing involving known sites or known introns at short or long distances
|
|
|
417 See README instructions for the distinction between known sites and known introns">
|
|
|
418 <option value="none" selected="true">None</option>
|
|
|
419 <option value="gmapdb">From the GMAP Database</option>
|
|
|
420 <option value="history">A Map in your history</option>
|
|
|
421 </param>
|
|
|
422 <when value="none"/>
|
|
|
423 <when value="history">
|
|
|
424 <param name="splicemap" type="data" format="splicesites.iit,introns.iit" metadata_name="dbkey" label="Select a splicesite map"
|
|
|
425 help="built with GMAP IIT"/>
|
|
|
426 <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites"
|
|
|
427 help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron.
|
|
|
428 This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>
|
|
|
429 </when>
|
|
|
430 <when value="gmapdb">
|
|
|
431 <param name="splicemap" type="select" data_ref="gmapdb" label="Use map for splicing involving known sites or known introns" help="">
|
|
|
432 <options>
|
|
|
433 <filter type="data_meta" ref="gmapdb" key="maps" multiple="True"/>
|
|
|
434 </options>
|
|
|
435 </param>
|
|
|
436 <param name="ambig_splice_noclip" type="boolean" checked="false" truevalue="--ambig-splice-noclip" falsevalue="" label="Do not clip at ambiguous splice sites"
|
|
|
437 help="For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend instead into the intron.
|
|
|
438 This flag makes sense only if you are trying to eliminate all soft clipping with --trim-mismatch-score=0"/>
|
|
|
439 </when>
|
|
|
440 </conditional>
|
|
|
441
|
|
|
442 <conditional name="use_snps">
|
|
|
443 <param name="src" type="select" label="<HR>Known SNPs" help="for SNP tolerant alignments">
|
|
|
444 <option value="none" selected="true">None</option>
|
|
|
445 <option value="gmapdb">From the GMAP Database</option>
|
|
|
446 <option value="history">A SNP Index in your history</option>
|
|
|
447 </param>
|
|
|
448 <when value="none"/>
|
|
|
449 <when value="history">
|
|
|
450 <param name="snpindex" type="data" format="gmapsnpindex" metadata_name="dbkey" label="Select a snpindex"
|
|
|
451 help="built with GMAP SNP Index"/>
|
|
|
452 </when>
|
|
|
453 <when value="gmapdb">
|
|
|
454 <param name="snpindex" type="select" data_ref="gmapdb" label="Use database containing known SNPs" help="">
|
|
|
455 <options>
|
|
|
456 <filter type="data_meta" ref="gmapdb" key="snps" multiple="True" separator=","/>
|
|
|
457 </options>
|
|
|
458 </param>
|
|
|
459 </when>
|
|
|
460 </conditional>
|
|
|
461
|
|
|
462 </when>
|
|
|
463 </conditional>
|
|
|
464
|
|
|
465 <!-- Computation options -->
|
|
|
466 <conditional name="computation">
|
|
|
467 <param name="options" type="select" label="<HR>Computational Settings" help="">
|
|
|
468 <option value="default">Use default settings</option>
|
|
|
469 <option value="advanced">Set Computation Options</option>
|
|
|
470 </param>
|
|
|
471 <when value="default"/>
|
|
|
472 <when value="advanced">
|
|
|
473 <param name="max_mismatches" type="float" value="" optional="true" label="Maximum number of mismatches allowed (uses default when negative)"
|
|
|
474 help="Defaults to the ultrafast level of ((readlength+2)/12 - 2)).
|
|
|
475 If specified between 0.0 and 1.0, then treated as a fraction
|
|
|
476 of each read length. Otherwise, treated as an integral number
|
|
|
477 of mismatches (including indel and splicing penalties)
|
|
|
478 For RNA-Seq, you may need to increase this value slightly
|
|
|
479 to align reads extending past the ends of an exon.">
|
|
|
480 <validator type="in_range" message="The mismatches must >= 0." min="0."/>
|
|
|
481 </param>
|
|
|
482 <param name="query_unk_mismatch" type="boolean" checked="false" truevalue="--query-unk-mismatch=1" falsevalue="" label="Count unknown (N) characters in the query as a mismatch"/>
|
|
|
483 <param name="genome_unk_mismatch" type="boolean" checked="true" truevalue="" falsevalue="--genome-unk-mismatch=0" label="Count unknown (N) characters in the genome as a mismatch"/>
|
|
|
484 <param name="terminal_threshold" type="integer" value="" optional="true" label="Threshold for searching for a terminal alignment (default 2)"
|
|
|
485 help="(from one end of the read to the best possible position at the other end). For example, if this value is 2, then if GSNAP finds an exact or
|
|
|
486 1-mismatch alignment, it will not try to find a terminal alignment.
|
|
|
487 Note that this default value may not be low enough if you want to
|
|
|
488 obtain terminal alignments for very short reads, although such reads
|
|
|
489 probably don't have enough specificity for terminal alignments anyway." />
|
|
|
490 <param name="indel_penalty" type="integer" value="" optional="true" label="Penalty for an indel (default 2)"
|
|
|
491 help="Counts against mismatches allowed. To find indels, make indel-penalty less than or equal to max-mismatches. A value < 2 can lead to false positives at read ends" />
|
|
|
492 <param name="indel_endlength" type="integer" value="" optional="true" label="Minimum length at end required for indel alignments (default 4)" />
|
|
|
493 <param name="max_middle_insertions" type="integer" value="" optional="true" label="Maximum number of middle insertions allowed (default 9)" />
|
|
|
494 <param name="max_middle_deletions" type="integer" value="" optional="true" label="Maximum number of middle deletions allowed (default 30)" />
|
|
|
495 <param name="max_end_insertions" type="integer" value="" optional="true" label="Maximum number of end insertions allowed (default 3)" />
|
|
|
496 <param name="max_end_deletions" type="integer" value="" optional="true" label="Maximum number of end deletions allowed (default 6)" />
|
|
|
497 <param name="suboptimal_levels" type="integer" value="" optional="true" label="Report suboptimal hits beyond best hit (default 0)"
|
|
|
498 help="All hits with best score plus suboptimal-levels are reported" />
|
|
|
499 <param name="adapter_strip" type="select" label="Method for removing adapters from reads"
|
|
|
500 help="paired removes adapters from paired-end reads if a concordant or paired alignment cannot be found from the original read">
|
|
|
501 <option value="paired" selected="true">paired</option>
|
|
|
502 <option value="off">off</option>
|
|
|
503 </param>
|
|
|
504 <param name="trim_mismatch_score" type="integer" value="" optional="true" label="Score to use for mismatches when trimming at ends (default is -3)"
|
|
|
505 help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive mismatches at the ends of reads)"/>
|
|
|
506 <param name="trim_indel_score" type="integer" value="" optional="true" label="Score to use for indels when trimming at ends (default is -4)"
|
|
|
507 help="to turn off trimming, specify 0 (Warning: turning trimming off will give false positive indels at the ends of reads)"/>
|
|
|
508 <param name="use_tally" type="data" format="tally.iit" optional="true" metadata_name="dbkey" label="Select a tally IIT file to resolve concordant multiple results"
|
|
|
509 help="generated by gsnap_tally and iit_store"/>
|
|
|
510
|
|
|
511 <!--
|
|
|
512 tallydir=STRING Directory for tally IIT file to resolve concordant multiple results (default is
|
|
|
513 location of genome index files specified using -D and -d). Note: can
|
|
|
514 just give full path name to use-tally instead.
|
|
|
515 use-tally=STRING Use this tally IIT file to resolve concordant multiple results
|
|
|
516 runlengthdir=STRING Directory for runlength IIT file to resolve concordant multiple results (default is
|
|
|
517 location of genome index files specified using -D and -d). Note: can
|
|
|
518 just give full path name to use-runlength instead.
|
|
|
519 use-runlength=STRING Use this runlength IIT file to resolve concordant multiple results
|
|
|
520 -->
|
|
|
521
|
|
|
522 <!-- Options for GMAP alignment within GSNAP -->
|
|
|
523 <param name="gmap_mode" type="select" multiple="true" optional="true" display="checkboxes" label="Cases to use GMAP for complex alignments containing multiple splices or indels"
|
|
|
524 help="Default: pairsearch,terminal,improve">
|
|
|
525 <option value="pairsearch" selected="true">pairsearch</option>
|
|
|
526 <option value="terminal" selected="true">terminal</option>
|
|
|
527 <option value="improve" selected="true">improve</option>
|
|
|
528 </param>
|
|
|
529 <param name="trigger_score_for_gmap" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 5)"
|
|
|
530 help="Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5)" />
|
|
|
531 <param name="max_gmap_pairsearch" type="integer" value="" optional="true" label="GMAP pairsearch threshold (default 3)"
|
|
|
532 help="Perform GMAP pairsearch on nearby genomic regions up to this many candidate ends (default 3)." />
|
|
|
533 <param name="max_gmap_terminal" type="integer" value="" optional="true" label="GMAP terminal threshold (default 3)"
|
|
|
534 help="Perform GMAP terminal on nearby genomic regions up to this many candidate ends (default 3)." />
|
|
|
535 <param name="max_gmap_improvement" type="integer" value="" optional="true" label="GMAP improvement threshold (default 3)"
|
|
|
536 help="Perform GMAP improvement on nearby genomic regions up to this many candidate ends (default 3)." />
|
|
|
537 <param name="microexon_spliceprob" type="float" value="" optional="true" label="GMAP microexons threshold (default .90)"
|
|
|
538 help="Allow microexons only if one of the splice site probabilities is greater than this value." >
|
|
|
539 <validator type="in_range" message="The microexons probability must be between 0. and 1." min="0." max="1."/>
|
|
|
540 </param>
|
|
|
541 </when>
|
|
|
542 </conditional>
|
|
|
543
|
|
|
544 <conditional name="splicing">
|
|
|
545 <param name="options" type="select" label="<HR>Splicing options for RNA-Seq" help="">
|
|
|
546 <option value="default">Use default settings</option>
|
|
|
547 <option value="advanced">Set Splicing Options</option>
|
|
|
548 </param>
|
|
|
549 <when value="default"/>
|
|
|
550 <when value="advanced">
|
|
|
551 <!-- Splicing options for RNA-Seq -->
|
|
|
552 <!-- use-splicing This should be either a select list from the gmapdb maps or a data type using splicesdir and use-splicing -->
|
|
|
553 <!-- Neither novel splicing (-N) nor known splicing (-s) turned on => assume reads are DNA-Seq (genomic) -->
|
|
|
554 <param name="novelsplicing" type="boolean" checked="false" truevalue="--novelsplicing=1" falsevalue="" label="Look for novel splicing "/>
|
|
|
555 <param name="localsplicedist" type="integer" value="" optional="true" label="Definition of local novel splicing event (default 200000)"/>
|
|
|
556 <param name="local_splice_penalty" type="integer" value="" optional="true" label="Penalty for a local splice (default 0). Counts against mismatches allowed"/>
|
|
|
557 <param name="distant_splice_penalty" type="integer" value="" optional="true" label="Penalty for a distant splice (default 3). Counts against mismatches allowed"
|
|
|
558 help="A distant splice is one where the intron length exceeds the value of localsplicedist or is an
|
|
|
559 inversion, scramble, or translocation between two different chromosomes. Counts against mismatches allowed"/>
|
|
|
560 <param name="distant_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for distant spliced alignments"
|
|
|
561 help="(default 16, min is the kmer length)"/>
|
|
|
562 <param name="shortend_splice_endlength" type="integer" value="" optional="true" label="Minimum length at end required for short-end spliced alignments"
|
|
|
563 help="(default 2, but unless known splice sites are provided, GSNAP may still need the end length to be the value of kmer size to find a given splice"/>
|
|
|
564 <param name="distant_splice_identity" type="float" value="" optional="true" label="Minimum identity at end required for distant spliced alignments (default 0.95)"/>
|
|
|
565 <param name="antistranded_penalty" type="integer" value="" optional="true" label="Penalty for antistranded splicing when using stranded RNA-Seq protocols"
|
|
|
566 help="A positive value, such as 1, expects antisense on the first read and sense on the second read.
|
|
|
567 Default is 0, which treats sense and antisense equally well"/>
|
|
|
568 </when>
|
|
|
569 </conditional>
|
|
|
570
|
|
|
571 <!-- Output data -->
|
|
|
572 <conditional name="output">
|
|
|
573 <param name="options" type="select" label="<HR><H2>Output</H2>Output options for RNA-Seq" help="">
|
|
|
574 <option value="default">Use default settings</option>
|
|
|
575 <option value="advanced">Set Output Options</option>
|
|
|
576 </param>
|
|
|
577 <when value="default"/>
|
|
|
578 <when value="advanced">
|
|
|
579 <param name="npath" type="integer" value="" optional="true" label="Maximum number of paths to print (default 100)"/>
|
|
|
580 <param name="quiet_if_excessive" type="boolean" checked="false" truevalue="--quiet-if-excessive" falsevalue="" label="Quiet if Excessive"
|
|
|
581 help="If more than maximum number of paths are found, then nothing is printed."/>
|
|
|
582 <param name="show_refdiff" type="boolean" checked="false" truevalue="--show-refdiff" falsevalue="" label="Show SNP-tolerant alignment"
|
|
|
583 help="For GSNAP output in SNP-tolerant alignment, shows all differences relative to the reference genome as lower case (otherwise, it shows all differences relative to both the reference and alternate genome)"/>
|
|
|
584 <param name="clip_overlap" type="boolean" checked="false" truevalue="--clip-overlap" falsevalue="" label="Clip Overlap"
|
|
|
585 help="For paired-end reads whose alignments overlap, clip the overlapping region."/>
|
|
|
586 </when>
|
|
|
587 </conditional>
|
|
|
588 <conditional name="result">
|
|
|
589 <param name="format" type="select" label="Select the output format" help="">
|
|
|
590 <option value="sam">SAM</option>
|
|
|
591 <!-- goby should only be an option if the input is in goby format
|
|
|
592 <option value="goby">Goby</option>
|
|
|
593 -->
|
|
|
594 <option value="gsnap">GSNAP default output</option>
|
|
|
595 </param>
|
|
|
596 <when value="gsnap">
|
|
|
597 </when>
|
|
|
598 <when value="sam">
|
|
|
599 <param name="no_sam_headers" type="boolean" truevalue="--no-sam-headers" falsevalue="" checked="false" label="Do not print headers beginning with '@'"/>
|
|
|
600 <param name="read_group_id" type="text" value="" optional="true" label="Value to put into read-group id (RG-ID) field"/>
|
|
|
601 <param name="read_group_name" type="text" value="" optional="true" label="Value to put into read-group name (RG-SM) field"/>
|
|
|
602 <param name="read_group_library" type="text" value="" optional="true" label="Value to put into read-group library (RG-LB) field"/>
|
|
|
603 <param name="read_group_platform" type="text" value="" optional="true" label="Value to put into read-group library platform (RG-PL) field"/>
|
|
|
604 <param name="quality_shift" type="integer" value="" optional="true" label="Shift FASTQ quality scores by this amount in SAM output (default -31)"/>
|
|
|
605 </when>
|
|
|
606 <!--
|
|
|
607 <when value="goby">
|
|
|
608 <param name="goby_output" type="text" value="" label="Basename for Goby output files"/>
|
|
|
609 <param name="creads_window_start" type="integer" value="" optional="true" label="Compact reads window start (default: 0=start of file)"/>
|
|
|
610 <param name="creads_window_end" type="integer" value="" optional="true" label="Compact reads window end (default: 0=end of file)"/>
|
|
|
611 <param name="creads_complement" type="boolean" truevalue="-\-creads-complement" falsevalue="" checked="false" label="Complement read sequences (without reversing)"/>
|
|
|
612 </when>
|
|
|
613 -->
|
|
|
614 </conditional>
|
|
|
615 <!-- TODO combine fails and split_output -->
|
|
|
616
|
|
|
617 <conditional name="results">
|
|
|
618 <param name="split_output" type="select" label="<HR>Split outputs"
|
|
|
619 help="Separate outputs for: nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult results">
|
|
|
620 <option value="no">no</option>
|
|
|
621 <option value="yes">yes</option>
|
|
|
622 </param>
|
|
|
623 <when value="no">
|
|
|
624 <conditional name="fails">
|
|
|
625 <param name="choice" type="select" label="How to deal with fails" help="">
|
|
|
626 <option value="default">default - include them in results</option>
|
|
|
627 <option value="nofails">nofails - exclude fails from results</option>
|
|
|
628 <option value="failsonly">failsonly - only output failing results</option>
|
|
|
629 </param>
|
|
|
630 <when value="default"/>
|
|
|
631 <when value="nofails"/>
|
|
|
632 <when value="failsonly">
|
|
|
633 <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format"
|
|
|
634 help=""/>
|
|
|
635 </when>
|
|
|
636 </conditional>
|
|
|
637 </when>
|
|
|
638 <when value="yes">
|
|
|
639 <conditional name="fails">
|
|
|
640 <param name="choice" type="select" label="How to deal with fails" help="">
|
|
|
641 <option value="default">default - include them in results</option>
|
|
|
642 <option value="nofails">nofails - exclude fails from results</option>
|
|
|
643 <option value="failsonly">failsonly - only output failing results</option>
|
|
|
644 </param>
|
|
|
645 <when value="default"/>
|
|
|
646 <when value="nofails"/>
|
|
|
647 <when value="failsonly"/>
|
|
|
648 </conditional>
|
|
|
649 <param name="fails_as_input" type="boolean" truevalue="--fails-as-input" falsevalue="" checked="false" label="Print completely failed alignments as input FASTA or FASTQ format"
|
|
|
650 help=""/>
|
|
|
651 </when>
|
|
|
652 </conditional>
|
|
|
653
|
|
|
654 </inputs>
|
|
|
655 <outputs>
|
|
|
656 <data format="txt" name="gsnap_stderr" label="${tool.name} on ${on_string}: gsnap.log"/>
|
|
|
657
|
|
|
658 <data format="txt" name="gsnap_out" label="${tool.name} on ${on_string} ${result.format}" >
|
|
|
659 <filter>(results['split_output'] == 'no' and (results['fails']['choice'] != 'failsonly' or results['fails']['fails_as_input'] == False))</filter>
|
|
|
660 <change_format>
|
|
|
661 <when input="result['format']" value="sam" format="sam"/>
|
|
|
662 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
663 </change_format>
|
|
|
664 </data>
|
|
|
665
|
|
|
666 <data format="fastq" name="gsnap_fq" label="${tool.name} on ${on_string} fails.fq" >
|
|
|
667 <filter>(results['split_output'] == 'no' and results['fails']['choice'] == 'failsonly' and results['fails']['fails_as_input'] == True)</filter>
|
|
|
668 </data>
|
|
|
669
|
|
|
670 <!-- nomapping, halfmapping_uniq, halfmapping_mult, unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, concordant_mult -->
|
|
|
671
|
|
|
672 <data format="txt" name="unpaired_mult" label="${tool.name} on ${on_string} unpaired_mult.${result.format}" from_work_dir="gsnap_out.unpaired_mult">
|
|
|
673 <filter>(results['split_output'] == 'yes')</filter>
|
|
|
674 <change_format>
|
|
|
675 <when input="result['format']" value="sam" format="sam"/>
|
|
|
676 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
677 </change_format>
|
|
|
678 </data>
|
|
|
679 <data format="txt" name="unpaired_uniq" label="${tool.name} on ${on_string} unpaired_uniq.${result.format}" from_work_dir="gsnap_out.unpaired_uniq">
|
|
|
680 <filter>(results['split_output'] == 'yes')</filter>
|
|
|
681 <change_format>
|
|
|
682 <when input="result['format']" value="sam" format="sam"/>
|
|
|
683 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
684 </change_format>
|
|
|
685 </data>
|
|
|
686 <data format="txt" name="unpaired_transloc" label="${tool.name} on ${on_string} unpaired_transloc.${result.format}" from_work_dir="gsnap_out.unpaired_transloc">
|
|
|
687 <filter>(results['split_output'] == 'yes')</filter>
|
|
|
688 <change_format>
|
|
|
689 <when input="result['format']" value="sam" format="sam"/>
|
|
|
690 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
691 </change_format>
|
|
|
692 </data>
|
|
|
693 <data format="txt" name="halfmapping_mult" label="${tool.name} on ${on_string} halfmapping_mult.${result.format}" from_work_dir="gsnap_out.halfmapping_mult">
|
|
|
694 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
695 <change_format>
|
|
|
696 <when input="result['format']" value="sam" format="sam"/>
|
|
|
697 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
698 </change_format>
|
|
|
699 </data>
|
|
|
700 <data format="txt" name="halfmapping_uniq" label="${tool.name} on ${on_string} halfmapping_uniq.${result.format}" from_work_dir="gsnap_out.halfmapping_uniq">
|
|
|
701 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
702 <change_format>
|
|
|
703 <when input="result['format']" value="sam" format="sam"/>
|
|
|
704 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
705 </change_format>
|
|
|
706 </data>
|
|
|
707 <data format="txt" name="halfmapping_transloc" label="${tool.name} on ${on_string} halfmapping_transloc.${result.format}" from_work_dir="gsnap_out.halfmapping_transloc">
|
|
|
708 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
709 <change_format>
|
|
|
710 <when input="result['format']" value="sam" format="sam"/>
|
|
|
711 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
712 </change_format>
|
|
|
713 </data>
|
|
|
714 <data format="txt" name="paired_mult" label="${tool.name} on ${on_string} paired_mult.${result.format}" from_work_dir="gsnap_out.paired_mult">
|
|
|
715 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
716 <change_format>
|
|
|
717 <when input="result['format']" value="sam" format="sam"/>
|
|
|
718 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
719 </change_format>
|
|
|
720 </data>
|
|
|
721 <data format="txt" name="paired_uniq" label="${tool.name} on ${on_string} paired_uniq.${result.format}" from_work_dir="gsnap_out.paired_uniq">
|
|
|
722 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
723 <change_format>
|
|
|
724 <when input="result['format']" value="sam" format="sam"/>
|
|
|
725 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
726 </change_format>
|
|
|
727 </data>
|
|
|
728 <data format="txt" name="paired_transloc" label="${tool.name} on ${on_string} paired_transloc.${result.format}" from_work_dir="gsnap_out.paired_transloc">
|
|
|
729 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
730 <change_format>
|
|
|
731 <when input="result['format']" value="sam" format="sam"/>
|
|
|
732 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
733 </change_format>
|
|
|
734 </data>
|
|
|
735
|
|
|
736 <data format="txt" name="concordant_mult" label="${tool.name} on ${on_string} concordant_mult.${result.format}" from_work_dir="gsnap_out.concordant_mult">
|
|
|
737 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
738 <change_format>
|
|
|
739 <when input="result['format']" value="sam" format="sam"/>
|
|
|
740 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
741 </change_format>
|
|
|
742 </data>
|
|
|
743 <data format="txt" name="concordant_uniq" label="${tool.name} on ${on_string} concordant_uniq.${result.format}" from_work_dir="gsnap_out.concordant_uniq">
|
|
|
744 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
745 <change_format>
|
|
|
746 <when input="result['format']" value="sam" format="sam"/>
|
|
|
747 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
748 </change_format>
|
|
|
749 </data>
|
|
|
750 <data format="txt" name="concordant_transloc" label="${tool.name} on ${on_string} concordant_transloc.${result.format}" from_work_dir="gsnap_out.concordant_transloc">
|
|
|
751 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
752 <change_format>
|
|
|
753 <when input="result['format']" value="sam" format="sam"/>
|
|
|
754 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
755 </change_format>
|
|
|
756 </data>
|
|
|
757
|
|
|
758 <data format="txt" name="nomapping" label="${tool.name} on ${on_string} nomapping.${result.format}" from_work_dir="gsnap_out.nomapping">
|
|
|
759 <filter>(results['split_output'] == 'yes' and results['fails_as_input'] == False)</filter>
|
|
|
760 <change_format>
|
|
|
761 <when input="result['format']" value="sam" format="sam"/>
|
|
|
762 <when input="result['format']" value="gsnap" format="gsnap"/>
|
|
|
763 </change_format>
|
|
|
764 </data>
|
|
|
765
|
|
|
766 <data format="fastq" name="nomapping_fq" label="${tool.name} on ${on_string} nomapping.fq" from_work_dir="gsnap_out.nomapping.fq">
|
|
|
767 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == False)</filter>
|
|
|
768 </data>
|
|
|
769
|
|
|
770 <data format="fastq" name="nomapping_1_fq" label="${tool.name} on ${on_string} nomapping.1.fq" from_work_dir="gsnap_out.nomapping.1.fq">
|
|
|
771 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
772 </data>
|
|
|
773
|
|
|
774 <data format="fastq" name="nomapping_2_fq" label="${tool.name} on ${on_string} nomapping.2.fq" from_work_dir="gsnap_out.nomapping.2.fq">
|
|
|
775 <filter>(results['split_output'] == 'yes' and seq['format'] == 'fastq' and seq['paired']['ispaired'] == True)</filter>
|
|
|
776 </data>
|
|
|
777
|
|
|
778 <!-- Will problay need wrapper code to generate composite datatype for goby alignment
|
|
|
779 <data format="gobyalignment" name="goby_alignment" label="${tool.name} on ${on_string} uniq.${result.format}" from_work_dir="gsnap_out.nomapping">
|
|
|
780 <filter>result['format'] == 'goby'</filter>
|
|
|
781 </data>
|
|
|
782 -->
|
|
|
783
|
|
|
784 </outputs>
|
|
|
785 <tests>
|
|
|
786 </tests>
|
|
|
787
|
|
|
788 <help>
|
|
|
789
|
|
|
790 **What it does**
|
|
|
791
|
|
|
792 GSNAP_ (Genomic Short-read Nucleotide Alignment Program) is a short read aligner which can align both single- and paired-end reads as short as 14nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state. It is developed by Thomas D. Wu of Genentech, Inc.
|
|
|
793 Publication_ citation: Thomas D. Wu, Serban Nacu "Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics. 2010 Apr 1;26(7):873-81. Epub 2010 Feb 10.
|
|
|
794
|
|
|
795 .. _GSNAP: http://research-pub.gene.com/gmap/
|
|
|
796 .. _Publication: http://bioinformatics.oupjournals.org/cgi/content/full/26/7/873
|
|
|
797 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2844994/?tool=pubmed
|
|
|
798
|
|
|
799 ------
|
|
|
800
|
|
|
801 **Know what you are doing**
|
|
|
802
|
|
|
803 .. class:: warningmark
|
|
|
804
|
|
|
805 You will want to read the README_
|
|
|
806
|
|
|
807 .. _README: http://research-pub.gene.com/gmap/src/README
|
|
|
808
|
|
|
809 ------
|
|
|
810
|
|
|
811 **Input formats**
|
|
|
812
|
|
|
813 Input to GSNAP should be either in FASTQ or FASTA format.
|
|
|
814
|
|
|
815 The FASTQ input may include quality scores, which will then be included in SAM
|
|
|
816 output, if that output format is selected.
|
|
|
817
|
|
|
818 For FASTA format, you should include one line per read (or end of a
|
|
|
819 paired-end read). The same FASTA file can have a mixture of
|
|
|
820 single-end and paired-end reads of varying lengths, if desired.
|
|
|
821
|
|
|
822 Single-end reads:
|
|
|
823
|
|
|
824 Each FASTA entry should contain one short read per line, like this
|
|
|
825
|
|
|
826 >Header information
|
|
|
827 AAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTA
|
|
|
828
|
|
|
829 Each short read can have a different length. However, the entire read
|
|
|
830 needs to be on a single line, and may not wrap around multiple lines.
|
|
|
831 If it extends to a second line, GSNAP will think that the read is
|
|
|
832 paired-end.
|
|
|
833
|
|
|
834
|
|
|
835 Paired-end reads:
|
|
|
836
|
|
|
837 Each FASTA entry should contain two short reads, one per line, like
|
|
|
838 this
|
|
|
839
|
|
|
840 >Header information
|
|
|
841 AAAACATTCTCCTCCGCATAAGCCTAGTAGATTA
|
|
|
842 GGCGTAGGTAGAAGTAGAGGTTAAGGCGCGTCAG
|
|
|
843
|
|
|
844 By default, the program assumes that the second end is in the reverse
|
|
|
845 complement direction compared with the first end. If they are in the
|
|
|
846 same direction, you may need to use the --circular-input (or -c) flag.
|
|
|
847
|
|
|
848 ( The Galaxy tool: "FASTA Width formatter" can be used to reformat fasta files to have single line sequences. )
|
|
|
849
|
|
|
850 ------
|
|
|
851
|
|
|
852 **Output formats in GSNAP**
|
|
|
853
|
|
|
854 SAM output format
|
|
|
855
|
|
|
856 Default GSNAP format
|
|
|
857 See the README_
|
|
|
858
|
|
|
859
|
|
|
860
|
|
|
861
|
|
|
862 </help>
|
|
|
863 </tool>
|
|
|
864
|
