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1 <tool id="segemehl" name="segemehl" version="0.1.6.0">
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2 <description>based short read aligner</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.6">segemehl</requirement>
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5 </requirements>
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6 <command>
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7 <![CDATA[
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8 ## prepare segemehl index if no reference genome is supplied
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9 temp_index = `mktemp`;
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10 #if $refGenomeSource.genomeSource == "history":
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11 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome;
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12 #else:
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13 #set $temp_index = ${refGenomeSource.index.fields.index_path}
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14 #end if
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15
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16
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17 ## execute segemehl
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18 segemehl.x
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19
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20 ## number of threads
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21 -t "\${GALAXY_SLOTS:-12}"
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22
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23 ## db file path
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24 -d ${refGenomeSource.index.fields.db_path}
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25
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26 -i $temp_index
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27
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28 ## check for single/pair-end
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29 #if str( $library.type ) == "single":
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30 #set $query_list = list()
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31 ## prepare inputs
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32 #for $fastq in $library.reads:
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33 $query_list.append('%s' %($fastq.input_query))
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34 #end for
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35 -q "#echo ' '.join( $query_list )#"
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36 #else
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37 ## prepare inputs
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38
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39 #set $mate1 = list()
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40 #set $mate2 = list()
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41 #for $mate_pair in $library.mate_list:
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42 $mate1.append( str($mate_pair.first_strand_query) )
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43 $mate2.append( str($mate_pair.second_strand_query) )
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44 #end for
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45
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46 -q #echo ','.join($mate1)
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47 -p #echo ','.join($mate2)
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48
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49 -I $library.maxinsertsize
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50 #end if
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51 -m $minsize
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52 -A $accuracy
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53 -H $hitstrategy
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54 #if str( $prime5 ).strip():
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55 -P $prime5
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56 #end if
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57 #if str( $prime3 ).strip():
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58 -Q $prime3
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59 #end if
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60 $polyA
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61 $autoclip
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62 $hardclip
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63 $order
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64 -s
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65 -o $segemehl_out
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66 ]]>
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67 </command>
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68 <stdio>
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69 <regex match="Exit forced"
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70 source="both"
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71 level="fatal"
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72 description="Execution halted." />
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73 </stdio>
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74 <inputs>
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75
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76 <conditional name="refGenomeSource">
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77 <param name="genomeSource" type="select" label="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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78 <option value="indexed">Use a built-in index</option>
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79 <option value="history">Use one from the history</option>
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80 </param>
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81 <when value="indexed">
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82 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
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83 <options from_data_table="segemehl_indexes">
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84 <column name="value" index="0"/>
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85 <column name="dbkey" index="1"/>
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86 <column name="name" index="2"/>
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87 <column name="db_path" index="3"/>
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88 <column name="index_path" index="4"/>
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89 <filter type="sort_by" column="2"/>
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90 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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91 </options>
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92 </param>
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93 </when> <!-- build-in -->
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94 <when value="history">
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95 <param name="own_reference_genome" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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96 </when> <!-- history -->
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97 </conditional> <!-- refGenomeSource -->
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98
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99
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100 <conditional name="library">
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101 <param name="type" type="select" label="Is this library paired-end?">
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102 <option value="single">Single-end</option>
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103 <option value="paired">Paired-end</option>
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104 </param>
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105 <when value="single">
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106 <repeat name="reads" title="FASTQ/FASTA files">
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107 <param name="input_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads fasta/fastq file" />
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108 </repeat>
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109 </when>
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110 <when value="paired">
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111 <repeat name="mate_list" title="Paired End Pairs" min="1">
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112 <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" />
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113 <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" />
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114 </repeat>
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115 <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000 (-I)" />
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116 </when>
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117 </conditional>
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118
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119
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120 <param name="minsize" type="integer" value="12" size="5" label="Minimum size of queries" help="default: 12 (-m)">
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121 <validator type="in_range" min="1"/>
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122 </param>
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123 <param name="accuracy" type="integer" value="85" size="5" label="Min percentage of matches per read in semi-global alignment" help="default: 85 (-A)" >
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124 <validator type="in_range" min="1" max="100"/>
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125 </param>
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126 <param name="hitstrategy" type="select" label="Hits to report?" help="(-H)">
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127 <option value="1">report only best scoring hits</option>
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128 <option value="0">report all scoring hits</option>
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129 </param>
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130 <param name="prime5" type="text" size="80" label="add 5' adapter" help="default: none (-Q)" />
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131 <param name="prime3" type="text" size="80" label="add 3' adapter" help="default: none (-P)"/>
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132 <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" help="(-T)"/>
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133 <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter" help="(-Y)"/>
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134 <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping" help="-C"/>
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135 <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" help="(-O)"/>
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136 </inputs>
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137
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138 <outputs>
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139 <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/>
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140 </outputs>
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141 <help>
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142 <![CDATA[
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143
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144 .. class:: infomark
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145
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146 **What it does**
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147
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148 Segemehl_ is a short read mapper with gaps.
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149
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150 Segemehl_ is a software to map short sequencer reads to reference genomes.
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151 Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions.
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152 Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly.
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153 segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl_ allows bisulfite sequencing mapping and split read mapping.
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154
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155 .. _Segemehl: http://www.bioinf.uni-leipzig.de/Software/segemehl/
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156
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157
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158 ]]>
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159 </help>
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160 <citations>
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161 <citation type="doi">10.1371/journal.pcbi.1000502</citation>
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162 </citations>
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163 </tool>
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