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1 <tool id="samtools_phase" name="Call and phase" version="1.0.0">
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2 <description>heterozygous SNPs</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.19">samtools</requirement>
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5 </requirements>
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6 <command>samtools phase -b "phase_wrapper"
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7 #if str($option_set.option_sets) == 'advanced':
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8 ${option_set.ignore_chimeras}
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9 -k $option_set.block_length
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10 -q $option_set.min_het
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11 -Q $option_set.min_bq
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12 -D $option_set.read_depth
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13 ${option_set.drop_ambiguous}
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14 #else
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15 -k 13 -q 37 -Q 13 -D 256
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16 #end if
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17 "$input_bam" > "$phase_sets"
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18 </command>
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19 <stdio>
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20 <exit_code range="1:" level="fatal" description="Error" />
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21 </stdio>
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22 <inputs>
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23 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
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24 <conditional name="option_set">
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25 <param name="option_sets" type="select" label="Phase parameters">
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26 <option value="default">Use defaults</option>
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27 <option value="advanced">Advanced options</option>
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28 </param>
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29 <when value="default" />
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30 <when value="advanced">
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31 <param name="block_length" type="integer" value="13" label="Maximum length for local phasing" />
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32 <param name="min_het" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
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33 <param name="min_bq" type="integer" value="13" label="Minimum base quality to be used in het calling" />
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34 <param name="read_depth" type="integer" value="256" label="Read depth" />
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35 <param name="ignore_chimeras" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
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36 <param name="drop_ambiguous" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
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37 </when>
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38 </conditional>
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39 </inputs>
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40 <outputs>
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41 <data format="txt" name="phase_sets" />
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42 <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" />
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43 <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
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44 <data format="bam" from_work_dir="phase_wrapper.chimeras.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="option_sets" value="default" />
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49 <param name="input_bam" value="samtools_phase_in_1.bam" />
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50 <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" />
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51 <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" />
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52 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" />
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53 <output name="chimera" file="empty_file.bam" compare="contains" />
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54 </test>
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55 <test>
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56 <param name="input_bam" value="samtools_phase_in_2.bam" />
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57 <param name="option_sets" value="advanced" />
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58 <param name="option_set|block_length" value="13" />
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59 <param name="option_set|min_het" value="37" />
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60 <param name="option_set|min_bq" value="13" />
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61 <param name="option_set|read_depth" value="256" />
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62 <param name="option_set|ignore_chimeras" value="false" />
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63 <param name="option_set|drop_ambiguous" value="true" />
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64 <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" />
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65 <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" />
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66 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" />
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67 <output name="chimera" file="empty_file.bam" compare="contains" />
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68 </test>
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69 <test>
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70 <param name="input_bam" value="samtools_phase_in_2.bam" />
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71 <param name="option_sets" value="advanced" />
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72 <param name="option_set|block_length" value="13" />
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73 <param name="option_set|min_het" value="37" />
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74 <param name="option_set|min_bq" value="13" />
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75 <param name="option_set|read_depth" value="256" />
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76 <param name="option_set|ignore_chimeras" value="true" />
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77 <param name="option_set|drop_ambiguous" value="false" />
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78 <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" />
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79 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" />
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80 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" />
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81 <output name="chimera" file="empty_file.bam" compare="contains" />
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82 </test>
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83 </tests>
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84 <help>
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85 **What it does**
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86
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87 Call and phase heterozygous SNPs
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88
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89 ------
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90
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91 .. list-table:: **Options**
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92 :widths: 5 5 40 10
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93 :header-rows: 1
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94
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95 * - Flag
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96 - Type
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97 - Description
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98 - Default
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99 * - -k
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100 - INT
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101 - Block length
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102 - 13
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103 * - -b
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104 - STR
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105 - Prefix of BAM file output
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106 - *null*
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107 * - -q
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108 - INT
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109 - Minimum het phred-LOD
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110 - 37
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111 * - -Q
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112 - INT
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113 - Min base quality in het calling
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114 - 13
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115 * - -D
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116 - INT
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117 - Max read depth
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118 - 256
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119 * - -D
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120 - BOOLEAN
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121 - Do not attempt to fix chimeras
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122 - *off*
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123 * - -A
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124 - BOOLEAN
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125 - Drop reads with ambiguous phase
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126 - *off*
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127
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128 ------
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129
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130 **Citation**
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131
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132 For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_
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133
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134
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135 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
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136
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137 </help>
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138 </tool>
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