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annotate picard_SamToFastq.xml @ 24:e65f2d5fd3d8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 92e89c89178482870c14cf15f38fbfd4470aa130"
author iuc
date Sat, 15 Jan 2022 12:38:18 +0000
parents 4740a2548206
children fdca9493e09b
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1 <tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
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2 <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>
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3 <macros>
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4 <import>picard_macros.xml</import>
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5 <token name="@WRAPPER_VERSION@">2</token>
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6 </macros>
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7 <xrefs>
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8 <xref type="bio.tools">picard_samtofastq</xref>
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9 </xrefs>
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10 <expand macro="requirements" />
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11 <command detect_errors="exit_code"><![CDATA[
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13 @java_options@
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14 @symlink_element_identifier@
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16 picard
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17 SamToFastq
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19 INPUT='$escaped_element_identifier'
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20
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21 #if str($single_or_paired) == "pe_interleaved":
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22 FASTQ='${interleaved_fastq}'
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23 INTERLEAVE=TRUE
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24 #else if str($single_or_paired) == "pe_sep":
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25 F='${fq1}'
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26 F2='${fq2}'
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27 FU='${fq_u}'
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28 #else
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29 F='${fq_single}'
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30 #end if
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32 RE_REVERSE="${re_reverse}"
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34 INCLUDE_NON_PF_READS="${include_non_pf_reads}"
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35 #if len(str($clipping_attribute)) > 0:
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36 CLIPPING_ATTRIBUTE="${clipping_attribute}"
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37 #end if
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38 #if len(str($clipping_action)) > 0:
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39 CLIPPING_ACTION="${clipping_action}"
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40 #end if
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41 READ1_TRIM="${read1_trim}"
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43 #if int($read1_max_bases_to_write) > -1:
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44 READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
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45 #end if
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47 READ2_TRIM="${read2_trim}"
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49 #if int($read2_max_bases_to_write) > -1:
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50 READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}"
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51 #end if
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53 INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
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55 VALIDATION_STRINGENCY="${validation_stringency}"
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56 QUIET=true
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57 VERBOSITY=ERROR
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58 @TMPDIR_OPTION@
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60 ]]></command>
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61 <inputs>
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63 <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>
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64 <param name="single_or_paired" type="select" label="Output format">
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65 <option value="se" >Single-end</option>
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66 <option value="pe_interleaved" selected="true">Paired-end (one interleaved output file)</option>
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67 <option value="pe_sep">Paired-end (two separate output files)</option>
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68 </param>
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69
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70 <param name="re_reverse" type="boolean" checked="True" label="Re-reverse bases and qualities of reads with negative strand flag set before writing them to fastq" help="RE_REVERSE; default=True"/>
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71 <param name="include_non_pf_reads" type="boolean" label="Include non-PF reads from the SAM/BAM dataset into the output FASTQ" help="INCLUDE_NON_PF_READS; PF means 'passes filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads; default=False"/>
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72 <param name="clipping_attribute" type="text" value="" label="The attribute that stores the position at which the SAM/BAM record should be clipped" help="CLIPPING_ATTRIBUTE; default=null"/>
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73 <param name="clipping_action" type="text" value="" label="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" help="CLIPPING_ACTION; default=null"/>
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74 <param name="read1_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 1" help="READ1_TRIM; default=0"/>
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75 <param name="read1_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 1 after trimming" help="READ1_MAX_BASES_TO_WRITE; 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=null (-1)"/>
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76 <param name="read2_trim" type="integer" value="0" min="0" label="The number of bases to trim from the beginning of read 2" help="READ2_TRIM; default=0"/>
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77 <param name="read2_max_bases_to_write" type="integer" value="-1" label="The maximum number of bases to write from read 2 after trimming" help="READ2_MAX_BASES_TO_WRITE; 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=null (-1)"/>
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78 <param name="include_non_primary_alignments" type="boolean" label="If true, include non-primary alignments in the output" help="INCLUDE_NON_PRIMARY_ALIGNMENTS; 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=False"/>
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80 <expand macro="VS" />
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82 </inputs>
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83
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84 <outputs>
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85 <data format="fastqsanger" name="fq_single" label="${tool.name} on ${on_string}: reads as fastq">
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86 <filter>output_type['single_or_paired'] == 'se'</filter>
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87 </data>
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88
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89 <data format="fastqsanger" name="interleaved_fastq" label="Interleaved pairs from ${tool.name} on ${on_string}">
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90 <filter>output_type['single_or_paired'] == 'pe_interleaved'</filter>
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91 </data>
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92
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93 <data format="fastqsanger" name="fq1" label="Paired-end forward strand from ${tool.name} on ${on_string}">
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94 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
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95 </data>
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96
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97 <data format="fastqsanger" name="fq2" label="Paired-end reverse strand from ${tool.name} on ${on_string}">
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98 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
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99 </data>
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100
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101 <data format="fastqsanger" name="fq_u" label="Paired-end unpaired reads from ${tool.name} on ${on_string}">
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102 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
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103 </data>
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104 </outputs>
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105
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106 <tests>
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107 <test>
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108 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
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109 <param name="single_or_paired" value="pe_interleaved" />
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110 <param name="output_per_rg" value="false"/>
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111 <param name="re_reverse" value="true"/>
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112 <param name="include_non_pf_reads" value="false"/>
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113 <param name="clipping_attribute" value="" />
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114 <param name="clipping_action" value="" />
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115 <param name="read1_trim" value="0" />
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116 <param name="read1_max_bases_to_write" value="-1"/>
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117 <param name="read2_trim" value="0" />
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118 <param name="read2_max_bases_to_write" value="-1"/>
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119 <param name="include_non_primary_alignments" value="false"/>
21
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120 <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
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121 </test>
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122 <test>
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123 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
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124 <param name="single_or_paired" value="pe_sep" />
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125 <param name="output_per_rg" value="false"/>
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126 <param name="re_reverse" value="true"/>
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127 <param name="include_non_pf_reads" value="false"/>
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128 <param name="clipping_attribute" value="" />
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129 <param name="clipping_action" value="" />
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130 <param name="read1_trim" value="0" />
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131 <param name="read1_max_bases_to_write" value="-1"/>
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132 <param name="read2_trim" value="0" />
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133 <param name="read2_max_bases_to_write" value="-1"/>
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134 <param name="include_non_primary_alignments" value="false"/>
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135 <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/>
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136 <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/>
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137 <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>
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138 </test>
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139 <test>
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140 <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
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141 <param name="single_or_paired" value="se" />
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142 <param name="output_per_rg" value="false"/>
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143 <param name="re_reverse" value="true"/>
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144 <param name="include_non_pf_reads" value="false"/>
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145 <param name="clipping_attribute" value="" />
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146 <param name="clipping_action" value="" />
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147 <param name="read1_trim" value="0" />
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148 <param name="read1_max_bases_to_write" value="-1"/>
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149 <param name="read2_trim" value="0" />
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150 <param name="read2_max_bases_to_write" value="-1"/>
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151 <param name="include_non_primary_alignments" value="false"/>
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152 <output name="fq_single" file="picard_SamToFastq_se.fq" ftype="fastqsanger"/>
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153 </test>
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154 </tests>
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155
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156
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157 <help>
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158
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159 **Purpose**
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160
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161 Extracts read sequences and qualities from the input SAM/BAM dataset and outputs them in Sanger fastq format. In the RE_REVERSE=True mode (default behavior), if the read is aligned and the alignment is to the reverse strand on the genome, the read's sequence from input SAM.BAM dataset 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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162
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163 -----
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164
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165 .. class:: warningmark
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166
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167 **DANGER: Multiple Outputs**
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168
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169 Generating per readgroup fastq (setting **OUTPUT_PER_RG** to True) may produce very large numbers of outputs. Know what you are doing!
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170
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171 @dataset_collections@
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172
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173 @description@
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174
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175 FASTQ=File
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176 F=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
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177 Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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178
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179 SECOND_END_FASTQ=File
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180 F2=File Output fastq file (if paired, second end of the pair fastq). Default value: null.
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181 Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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182
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183 UNPAIRED_FASTQ=File
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184 FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default
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185 value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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186
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187 OUTPUT_PER_RG=Boolean
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188 OPRG=Boolean Output a fastq file per read group (two fastq files per read group if the group is
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189 paired). Default value: false. Possible values: {true, false} Cannot be used in
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190 conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F)
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191
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192 OUTPUT_DIR=File
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193 ODIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true.
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194 Default value: null.
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195
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196 RE_REVERSE=Boolean
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197 RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them
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198 to fastq Default value: true. Possible values: {true, false}
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199
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200 INTERLEAVE=Boolean
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201 INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe
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202 which end it came from Default value: false. Possible values: {true, false}
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203
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204 INCLUDE_NON_PF_READS=Boolean
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205 NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes
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206 filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads.
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207 Default value: false. Possible values: {true, false}
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208
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209 CLIPPING_ATTRIBUTE=String
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210 CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default
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211 value: null.
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212
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213 CLIPPING_ACTION=String
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214 CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities
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215 should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in
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216 the clipped region; and any integer means that the base qualities should be set to that
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217 value in the clipped region. Default value: null.
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218
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219 READ1_TRIM=Integer
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220 R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0.
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221
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222 READ1_MAX_BASES_TO_WRITE=Integer
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223 R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than
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224 this many bases left after trimming, all will be written. If this value is null then all
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225 bases left after trimming will be written. Default value: null.
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226
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227 READ2_TRIM=Integer
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228 R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0.
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229
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230 READ2_MAX_BASES_TO_WRITE=Integer
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231 R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than
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232 this many bases left after trimming, all will be written. If this value is null then all
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233 bases left after trimming will be written. Default value: null.
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234
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235 INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean
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236 If true, include non-primary alignments in the output. Support of non-primary alignments
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237 in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and
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238 there are paired reads with non-primary alignments. Default value: false.
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239 Possible values: {true, false}
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240
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241 @more_info@
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242
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243 </help>
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244 <expand macro="citations" />
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245 </tool>