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1 <tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.1" force_history_refresh="True">
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2 <description>creates a FASTQ file</description>
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3 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
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4 <!-- Dan Blankenberg -->
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5 <command interpreter="python">picard_SamToFastq_wrapper.py
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6 -p '
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7 java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
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8 -jar "\$JAVA_JAR_PATH/SamToFastq.jar"
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9 INPUT="${input_sam}"
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10 VALIDATION_STRINGENCY="LENIENT"
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11 RE_REVERSE=${re_reverse}
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12 INCLUDE_NON_PF_READS=${include_non_pf_reads}
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13 #if str( $clipping_attribute ):
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14 CLIPPING_ATTRIBUTE="${clipping_attribute}"
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15 #end if
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16 #if str( $clipping_action ):
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17 CLIPPING_ACTION="${clipping_action}"
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18 #end if
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19 #if str( $read1_trim ):
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20 READ1_TRIM="${read1_trim}"
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21 #end if
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22 #if str( $read1_max_bases_to_write ):
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23 READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
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24 #end if
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25 INCLUDE_NON_PRIMARY_ALIGNMENTS=${include_non_primary_alignments}
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26
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27 #if str( $output_per_read_group_selector ) == 'per_sam_file':
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28 ##OUTPUT_PER_RG=false
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29 FASTQ="${output_fastq1}"
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30
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31 #if str( $single_paired_end_type.single_paired_end_type_selector ) == 'paired':
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32 SECOND_END_FASTQ="${output_fastq2}"
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33 #if str( $single_paired_end_type.read2_trim ):
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34 READ2_TRIM="${single_paired_end_type.read2_trim}"
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35 #end if
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36 #if str( $single_paired_end_type.read2_max_bases_to_write ):
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37 READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"
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38 #end if
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39 #end if
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40 '
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41 #else:
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42 OUTPUT_PER_RG=true
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43 #if str( $single_paired_end_type.single_paired_end_type_selector ) == 'paired':
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44 '
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45 --read_group_file_2 "${output_fastq2}"
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46 --file_id_2 "${output_fastq2.id}"
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47 -p '
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48 #if str( $single_paired_end_type.read2_trim ):
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49 READ2_TRIM="${single_paired_end_type.read2_trim}"
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50 #end if
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51 #if str( $single_paired_end_type.read2_max_bases_to_write ):
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52 READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"
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53 #end if
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54 #end if
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55 '
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56 --read_group_file_1 "${output_fastq1}"
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57 --new_files_path "${$__new_file_path__}"
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58 --file_id_1 "${output_fastq1.id}"
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59 #end if
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60 </command>
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61 <inputs>
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62 <param name="input_sam" type="data" format="sam,bam" label="BAM/SAM file" />
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63 <param name="read1_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 1." />
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64 <param name="read1_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 1 after trimming." />
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65 <param name="output_per_read_group_selector" type="select" label="Output per read group">
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66 <option value="per_sam_file" selected="True">Per BAM/SAM file</option>
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67 <option value="per_read_group">Per Read Group</option>
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68 </param>
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69 <conditional name="single_paired_end_type">
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70 <param name="single_paired_end_type_selector" type="select" label="Single or Paired end">
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71 <option value="single" selected="True">Single</option>
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72 <option value="paired">Paired end</option>
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73 </param>
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74 <when value="single">
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75 <!-- nothing yet -->
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76 </when>
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77 <when value="paired">
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78 <param name="read2_trim" type="integer" value="" optional="True" label="The number of bases to trim from the beginning of read 2." />
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79 <param name="read2_max_bases_to_write" type="integer" optional="True" value="" label="The maximum number of bases to write from read 2 after trimming." />
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80 </when>
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81 </conditional>
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82 <param name="re_reverse" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Re-reverse bases and qualities of reads on negative strand"/>
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83 <param name="include_non_pf_reads" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Include non-PF reads from the SAM file into the output FASTQ files."/>
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84 <param name="clipping_attribute" type="text" value="" label="The attribute that stores the position at which the SAM record should be clipped" help="Leave blank for null" />
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85 <param name="clipping_action" type="text" value="" label="The action that should be taken with clipped reads" help="'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Leave blank for null" />
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86 <param name="include_non_primary_alignments" type="boolean" truevalue="true" falsevalue="false" checked="False" label="If true, include non-primary alignments in the output." help="Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments."/>
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87
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88 </inputs>
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89 <outputs>
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90 <data format="fastqsanger" name="output_fastq1" label="${tool.name} on ${on_string}: FASTQ 1" />
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91 <data format="fastqsanger" name="output_fastq2" label="${tool.name} on ${on_string}: FASTQ 2" >
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92 <filter>single_paired_end_type['single_paired_end_type_selector'] == 'paired'</filter>
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93 </data>
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94 </outputs>
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95 <tests>
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96 <test>
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97 <param name="input_sam" value="bfast_out1.sam" ftype="sam" />
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98 <param name="output_per_read_group_selector" value="per_sam_file" />
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99 <param name="single_paired_end_type_selector" value="single" />
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100 <param name="read1_trim" value="" />
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101 <param name="read1_max_bases_to_write" value="" />
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102 <param name="re_reverse" value="True" />
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103 <param name="include_non_pf_reads" value="False" />
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104 <param name="clipping_action" value="" />
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105 <param name="clipping_attribute" value="" />
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106 <param name="include_non_primary_alignments" value="False" />
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107 <output name="output_fastq1" file="random_phiX_1.fastqsanger"/>
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108 </test>
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109 <test>
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110 <param name="input_sam" value="bwa_wrapper_out3.sam" ftype="sam" />
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111 <param name="output_per_read_group_selector" value="per_sam_file" />
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112 <param name="single_paired_end_type_selector" value="paired" />
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113 <param name="read1_trim" value="" />
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114 <param name="read1_max_bases_to_write" value="" />
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115 <param name="read2_trim" value="" />
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116 <param name="read2_max_bases_to_write" value="" />
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117 <param name="re_reverse" value="True" />
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118 <param name="include_non_pf_reads" value="False" />
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119 <param name="clipping_action" value="" />
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120 <param name="clipping_attribute" value="" />
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121 <param name="include_non_primary_alignments" value="False" />
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122 <output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
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123 <output name="output_fastq2" file="bwa_wrapper_in3.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
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124 </test>
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125 <test>
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126 <param name="input_sam" value="bwa_wrapper_out3.sam" ftype="sam" />
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127 <param name="output_per_read_group_selector" value="per_read_group" />
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128 <param name="single_paired_end_type_selector" value="paired" />
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129 <param name="read1_trim" value="" />
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130 <param name="read1_max_bases_to_write" value="" />
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131 <param name="read2_trim" value="" />
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132 <param name="read2_max_bases_to_write" value="" />
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133 <param name="re_reverse" value="True" />
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134 <param name="include_non_pf_reads" value="False" />
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135 <param name="clipping_action" value="" />
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136 <param name="clipping_attribute" value="" />
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137 <param name="include_non_primary_alignments" value="False" />
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138 <output name="output_fastq1" file="bwa_wrapper_in2.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
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139 <output name="output_fastq2" file="bwa_wrapper_in3.fastqsanger" lines_diff="64"/> <!-- 16 unaligned fastq blocks not present in original sam file -->
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140 </test>
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141 </tests>
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142 <help>
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143 **What it does**
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144
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145 Picard: SamToFastq converts SAM files to FASTQ files.
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146
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147 Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger fastq format. In the RC mode (default is True), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM file will be reverse-complemented prior to writing it to fastq in order restore correctly the original read sequence as it was generated by the sequencer.
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148
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149 ------
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150
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151 Please cite the website "http://picard.sourceforge.net".
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152
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153 ------
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154
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155
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156 **Input formats**
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157
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158 FastqToSam accepts SAM input files, see http://samtools.sourceforge.net for more details.
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159
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160 ------
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161
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162 **Outputs**
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163
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164 The output is in FASTQ format. If using Paired end data, 2 fastq files are created.
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165
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166 -------
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167
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168 **FastqToSam settings**
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169
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170 This is list of SamToFastq options::
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171
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172 INPUT=File Input SAM/BAM file to extract reads from Required.
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173 FASTQ=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq). Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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174 SECOND_END_FASTQ=File Output fastq file (if paired, second end of the pair fastq). Default value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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175 OUTPUT_PER_RG=Boolean Output a fastq file per read group (two fastq files per read group if the group is paired). Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} Cannot be used in conjuction with option(s) SECOND_END_FASTQ (F2) FASTQ (F)
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176 OUTPUT_DIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true. Default value: null.
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177 RE_REVERSE=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq Default value: true. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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178 INCLUDE_NON_PF_READS=Boolean Include non-PF reads from the SAM file into the output FASTQ files. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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179 CLIPPING_ATTRIBUTE=String The attribute that stores the position at which the SAM record should be clipped Default value: null.
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180 CLIPPING_ACTION=String The action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Default value: null.
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181 READ1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. This option can be set to 'null' to clear the default value.
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182 READ1_MAX_BASES_TO_WRITE=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
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183 READ2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. This option can be set to 'null' to clear the default value.
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184 READ2_MAX_BASES_TO_WRITE=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.
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185 INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean If true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false}
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186
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187
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188 </help>
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189 </tool>
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