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annotate picard_SamToFastq.xml @ 26:9ffcddf6f9c0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit cbe534af56ee782e8d1aa0fa872059d2a5e42db8"
author iuc
date Mon, 17 Feb 2020 10:24:29 -0500
parents 2a17c789e0a5
children 881d7645d1bf
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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 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9
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10 @java_options@
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11 @symlink_element_identifier@
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12
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13 picard
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14 SamToFastq
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16 INPUT='$escaped_element_identifier'
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18 #if str($single_or_paired) == "pe_interleaved":
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19 FASTQ='${interleaved_fastq}'
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20 INTERLEAVE=TRUE
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21 #else if str($single_or_paired) == "pe_sep":
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22 F='${fq1}'
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23 F2='${fq2}'
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24 FU='${fq_u}'
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25 #else
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26 F='${fq_single}'
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27 #end if
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29 RE_REVERSE="${re_reverse}"
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30
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31 INCLUDE_NON_PF_READS="${include_non_pf_reads}"
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32 #if len(str($clipping_attribute)) > 0:
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33 CLIPPING_ATTRIBUTE="${clipping_attribute}"
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34 #end if
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35 #if len(str($clipping_action)) > 0:
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36 CLIPPING_ACTION="${clipping_action}"
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37 #end if
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38 READ1_TRIM="${read1_trim}"
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39
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40 #if int($read1_max_bases_to_write) > -1:
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41 READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
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42 #end if
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43
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44 READ2_TRIM="${read2_trim}"
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45
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46 #if int($read2_max_bases_to_write) > -1:
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47 READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}"
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48 #end if
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49
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50 INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
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51
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52 VALIDATION_STRINGENCY="${validation_stringency}"
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53 QUIET=true
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54 VERBOSITY=ERROR
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55 @TMPDIR_OPTION@
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57 ]]></command>
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58 <inputs>
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60 <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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61 <param name="single_or_paired" type="select" label="Output format">
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62 <option value="se" >Single-end</option>
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63 <option value="pe_interleaved" selected="true">Paired-end (one interleaved output file)</option>
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64 <option value="pe_sep">Paired-end (two separate output files)</option>
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65 </param>
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66
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67 <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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68 <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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69 <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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70 <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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71 <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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72 <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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73 <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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74 <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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75 <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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77 <expand macro="VS" />
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79 </inputs>
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81 <outputs>
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82 <data format="fastqsanger" name="fq_single" label="${tool.name} on ${on_string}: reads as fastq">
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83 <filter>output_type['single_or_paired'] == 'se'</filter>
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84 </data>
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86 <data format="fastqsanger" name="interleaved_fastq" label="Interleaved pairs from ${tool.name} on ${on_string}">
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87 <filter>output_type['single_or_paired'] == 'pe_interleaved'</filter>
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88 </data>
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90 <data format="fastqsanger" name="fq1" label="Paired-end forward strand from ${tool.name} on ${on_string}">
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91 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
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92 </data>
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94 <data format="fastqsanger" name="fq2" label="Paired-end reverse strand from ${tool.name} on ${on_string}">
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95 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
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96 </data>
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97
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98 <data format="fastqsanger" name="fq_u" label="Paired-end unpaired reads from ${tool.name} on ${on_string}">
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99 <filter>output_type['single_or_paired'] == 'pe_sep'</filter>
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100 </data>
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101 </outputs>
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102
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103 <tests>
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104 <test>
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105 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
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106 <param name="single_or_paired" value="pe_interleaved" />
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107 <param name="output_per_rg" value="false"/>
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108 <param name="re_reverse" value="true"/>
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109 <param name="include_non_pf_reads" value="false"/>
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110 <param name="clipping_attribute" value="" />
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111 <param name="clipping_action" value="" />
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112 <param name="read1_trim" value="0" />
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113 <param name="read1_max_bases_to_write" value="-1"/>
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114 <param name="read2_trim" value="0" />
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115 <param name="read2_max_bases_to_write" value="-1"/>
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116 <param name="include_non_primary_alignments" value="false"/>
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117 <output name="interleaved_fastq" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
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118 </test>
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119 <test>
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120 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
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121 <param name="single_or_paired" value="pe_sep" />
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122 <param name="output_per_rg" value="false"/>
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123 <param name="re_reverse" value="true"/>
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124 <param name="include_non_pf_reads" value="false"/>
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125 <param name="clipping_attribute" value="" />
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126 <param name="clipping_action" value="" />
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127 <param name="read1_trim" value="0" />
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128 <param name="read1_max_bases_to_write" value="-1"/>
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129 <param name="read2_trim" value="0" />
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130 <param name="read2_max_bases_to_write" value="-1"/>
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131 <param name="include_non_primary_alignments" value="false"/>
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132 <output name="fq1" file="picard_SamToFastq_1.fq" ftype="fastqsanger"/>
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133 <output name="fq2" file="picard_SamToFastq_2.fq" ftype="fastqsanger"/>
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134 <output name="fq_u" file="picard_SamToFastq_u.fq" ftype="fastqsanger"/>
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135 </test>
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136 <test>
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137 <param name="inputFile" value="picard_SamToFastq_se.bam" ftype="bam"/>
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138 <param name="single_or_paired" value="se" />
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139 <param name="output_per_rg" value="false"/>
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140 <param name="re_reverse" value="true"/>
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141 <param name="include_non_pf_reads" value="false"/>
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142 <param name="clipping_attribute" value="" />
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143 <param name="clipping_action" value="" />
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144 <param name="read1_trim" value="0" />
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145 <param name="read1_max_bases_to_write" value="-1"/>
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146 <param name="read2_trim" value="0" />
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147 <param name="read2_max_bases_to_write" value="-1"/>
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148 <param name="include_non_primary_alignments" value="false"/>
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149 <output name="fq_single" file="picard_SamToFastq_se.fq" ftype="fastqsanger"/>
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150 </test>
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151 </tests>
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152
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153
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154 <help>
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155
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156 **Purpose**
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157
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158 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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159
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160 -----
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161
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162 .. class:: warningmark
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163
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164 **DANGER: Multiple Outputs**
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165
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166 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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167
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168 @dataset_collections@
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169
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170 @description@
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171
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172 FASTQ=File
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173 F=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
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174 Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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175
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176 SECOND_END_FASTQ=File
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177 F2=File Output fastq file (if paired, second end of the pair fastq). Default value: null.
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178 Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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179
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180 UNPAIRED_FASTQ=File
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181 FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default
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182 value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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183
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184 OUTPUT_PER_RG=Boolean
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185 OPRG=Boolean Output a fastq file per read group (two fastq files per read group if the group is
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186 paired). Default value: false. Possible values: {true, false} Cannot be used in
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187 conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F)
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188
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189 OUTPUT_DIR=File
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190 ODIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true.
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191 Default value: null.
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192
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193 RE_REVERSE=Boolean
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194 RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them
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195 to fastq Default value: true. Possible values: {true, false}
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196
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197 INTERLEAVE=Boolean
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198 INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe
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199 which end it came from Default value: false. Possible values: {true, false}
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200
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201 INCLUDE_NON_PF_READS=Boolean
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202 NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes
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203 filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads.
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204 Default value: false. Possible values: {true, false}
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205
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206 CLIPPING_ATTRIBUTE=String
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207 CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default
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208 value: null.
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209
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210 CLIPPING_ACTION=String
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211 CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities
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212 should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in
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213 the clipped region; and any integer means that the base qualities should be set to that
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214 value in the clipped region. Default value: null.
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215
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216 READ1_TRIM=Integer
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217 R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0.
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218
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219 READ1_MAX_BASES_TO_WRITE=Integer
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220 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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221 this many bases left after trimming, all will be written. If this value is null then all
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222 bases left after trimming will be written. Default value: null.
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223
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224 READ2_TRIM=Integer
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225 R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0.
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226
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227 READ2_MAX_BASES_TO_WRITE=Integer
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228 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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229 this many bases left after trimming, all will be written. If this value is null then all
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230 bases left after trimming will be written. Default value: null.
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231
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232 INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean
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233 If true, include non-primary alignments in the output. Support of non-primary alignments
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234 in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and
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235 there are paired reads with non-primary alignments. Default value: false.
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236 Possible values: {true, false}
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237
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238 @more_info@
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239
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240 </help>
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241 <expand macro="citations" />
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242 </tool>