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1 <tool id="microsatellite" name="STR detection" version="1.0.0">
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0
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2 <description>for short read, reference, and mapped data</description>
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3 <command interpreter="python2.7"> microsatellite.py
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4 "${filePath}"
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5 #if $inputFileSource.inputFileType == "fasta"
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6 --fasta
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7 #elif $inputFileSource.inputFileType == "fastq"
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8 --fastq
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9 #elif $inputFileSource.inputFileType == "fastq_noquals"
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10 --fastq:noquals
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11 #elif $inputFileSource.inputFileType == "sam"
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12 --sam
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13 #end if
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14
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15 #if $inputFileSource.inputFileType == "sam"
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16 #if $inputFileSource.referenceFileSource.requireReference
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17 --r --ref="${inputFileSource.referenceFileSource.referencePath}"
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18 #end if
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19 #end if
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20
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21 --period="${period}"
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22
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23 #if $partialmotifs == "true"
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24 --partialmotifs
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25 #end if
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26
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27 --minlength="${minlength}"
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28
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29
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30 --prefix="${prefix}"
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31 --suffix="${surfix}"
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32
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33 --hamming="${hammingThreshold}"
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34
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35 #if $multipleruns
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36 --multipleruns
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37 #end if
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38
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39 #if $flankSetting.noflankdisplay
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40 --noflankdisplay
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41 #else
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42 --flankdisplay=${flankSetting.flankdisplay}
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43 #end if
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44 > $stdout
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45 </command>
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46
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47 <inputs>
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48 <param name="filePath" label="Select input file" type="data"/>
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49 <conditional name="inputFileSource">
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50 <param name="inputFileType" type="select" label="Select input file type">
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51 <option value="fasta">Fasta File</option>
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52 <option value="fastq">Fastq File</option>
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53 <option value="fastq_noquals">Fastq File without Quality Information</option>
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54 <option value="sam">SAM File</option>
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55 </param>
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56 <when value="sam">
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57 <conditional name="referenceFileSource">
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58 <param name="requireReference" label="Do you want to extract correspond microsatellites in reference for comparison?" type="boolean">
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59 </param>
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60 <when value="true">
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61 <param name="referencePath" label="Select reference file" type="data"/>
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62 </when>
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63 </conditional>
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64 </when>
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65 </conditional>
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66
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67 <param name="period" label="Motif size of microsatellites of interest (e.g. Mononucleotide microsatellite =1) (must be less than 10)" type="integer" size="2" value="1"/>
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68 <param name="partialmotifs" label="Consider microsatellites with a partial motif?" type="boolean" checked="True"/>
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69 <param name="minlength" label="Minimal length (bp) of microsatellite sequence reported" type="integer" size="2" value="5"/>
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70
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71
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72 <param name="prefix" label="Do not report candidate repeat intervals that have left flanking region less than (bp):" type="integer" size="4" value="20"/>
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73 <param name="surfix" label="Do not report candidate repeat intervals that have left flanking region less than (bp):" type="integer" size="4" value="20"/>
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74
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75
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76 <param name="hammingThreshold" label="Hamming threshold of microsatellite, If greater than 0, interrupted microsatellites will also be reported" type="integer" size="2" value="0"/>
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77 <param name="multipleruns" label="Consider all candidate intervals in a sequence. If not check, only the longest one will be considered" type="boolean" checked="True"> </param>
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78 <conditional name="flankSetting">
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79 <param name="noflankdisplay" label="Show the entire flanking regions" type="boolean" checked="True"/>
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80 <when value="false">
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81 <param name="flankdisplay" label="Limit length (bp) of flanking regions shown" type="integer" size="4" value="5"/>
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82 </when>
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83 </conditional>
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84
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85 </inputs>
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86 <outputs>
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87 <data name="stdout" format="tabular"/>
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88 </outputs>
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89 <tests>
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90 <!-- Test data with valid values -->
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91 <test>
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92 <param name="filePath" value="C_sample_fastq"/>
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93 <param name="period" value="1"/>
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94 <param name="partialmotifs" value="true" />
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95 <param name="minlength" value="3" />
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96 <param name="prefix" value="5"/>
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97 <param name="surfix" value="5"/>
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98 <param name="hammingThreshold" value="0"/>
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99 <param name="multipleruns" value="true"> </param>
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100 <output name="microsatellite" file="C_sample_snoope"/>
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101 </test>
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102
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103 </tests>
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104 <help>
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105
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106
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107 .. class:: infomark
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108
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109 **What it does**
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110
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111 This tool identifies simple as well interrupted STRs. Choosing a hamming distance of zero will return simple STRs.
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112 Choosing a hamming distance of greater than zero will return both simple and interrupted STRs.
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113 The algorithms used to identify simple and interrupted STRs are described oin the manuscript cited below (see TABLE XXXX).
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114
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115 **Citation**
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116
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117 When you use this tool, please cite **Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research**
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118 This tool is developed by Chen Sun (cxs1031@cse.psu.edu) and Bob Harris (rsharris@bx.psu.edu)
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119
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120 **Input**
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121
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122 - The input files can be fastq, fasta, fastq without quality score, and SAM format.
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123
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124 **Output**
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125
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126 For fastq, the output will contain the following columns:
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127
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128 - Column 1 = length of STR (bp)
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129 - Column 2 = length of left flanking region (bp)
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130 - Column 3 = length of right flanking region (bp)
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131 - Column 4 = repeat motif (bp)
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132 - Column 5 = hamming distance
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133 - Column 6 = read name
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134 - Column 7 = read sequence with soft masking of STR
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135 - Column 8 = read quality (the same Phred score scale as input)
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136
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137 For fasta, fastq without quality score and sam format, column 8 will be replaced with dot(.).
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138
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139 If the users have mapped file (SAM) and would like to profile STRs from premapped data instead of using flank-based mapping approach, they can select SAM format input and specify that they want correspond STRs in reference for comparison. The output will be as follow:
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140
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141 - Column 1 = length of STR (bp)
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142 - Column 2 = length of left flanking region (bp)
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143 - Column 3 = length of right flanking region (bp)
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144 - Column 4 = repeat motif (bp)
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145 - Column 5 = hamming distance
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146 - Column 6 = read name
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147 - Column 7 = read sequence with soft masking of STR
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148 - Column 8 = read quality (the same Phred score scale as input)
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149 - Column 9 = read name (The same as column 6)
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150 - Column 10 = chromosome
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151 - Column 11 = left flanking region start
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152 - Column 12 = left flanking region stop
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153 - Column 13 = STR start as infer from pair-end
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154 - Column 14 = STR stop as infer from pair-end
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155 - Column 15 = right flanking region start
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156 - Column 16 = right flanking region stop
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157 - Column 17 = STR length in reference
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158 - Column 18 = STR sequence in reference
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159
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160 </help>
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161 </tool>
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