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annotate picard_SamToFastq.xml @ 4:2589e6207cb4 draft

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author devteam
date Tue, 13 Oct 2015 12:27:49 -0400
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children 08f69add4d06
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1 <tool name="SamToFastq" id="picard_SamToFastq" version="@TOOL_VERSION@.0">
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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 </macros>
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6 <expand macro="requirements" />
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7 <command>
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9 echo "BAM" > $report &amp;&amp; ## This is necessary for output dataset detection (see output tags below)
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11 @java_options@
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13 java -jar \$JAVA_JAR_PATH/picard.jar
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14 SamToFastq
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16 INPUT="${inputFile}"
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18 #if str( $output_per_rg ) == "true":
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19 OUTPUT_PER_RG=true
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20 OUTPUT_DIR=.
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21 #elif str( $output_per_rg ) == "false" and str( $interleave ) == "false":
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22 FASTQ=READ1.fastq
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23 SECOND_END_FASTQ=READ2.fastq
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24 UNPAIRED_FASTQ=UNPAIRED_READS.fastq
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25 #elif str( $output_per_rg ) == "false" and str( $interleave ) == "true":
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26 FASTQ=INTERLEAVED.fastq
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27 #end if
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29 RE_REVERSE="${re_reverse}"
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30 INTERLEAVE="${interleave}"
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31 INCLUDE_NON_PF_READS="${include_non_pf_reads}"
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32 CLIPPING_ATTRIBUTE="${clipping_attribute}"
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33 CLIPPING_ACTION="${clipping_action}"
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34 READ1_TRIM="${read1_trim}"
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36 #if int($read1_max_bases_to_write) > -1:
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37 READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"
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38 #end if
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40 READ2_TRIM="${read2_trim}"
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42 #if int($read2_max_bases_to_write) > -1:
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43 READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}"
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44 #end if
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46 INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"
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49 VALIDATION_STRINGENCY="${validation_stringency}"
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50 QUIET=true
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51 VERBOSITY=ERROR
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52
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53 </command>
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54 <inputs>
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55
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56 <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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57 <param name="output_per_rg" type="boolean" checked="False" label="Do you want to output a fastq file per read group (two fastq files per read group if the group is paired)" help="OUTPUT_PER_RG; default=False"/>
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58 <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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59 <param name="interleave" type="boolean" label="Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe which end it came from" help="INTERLEAVE; default=False"/>
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60 <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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61 <param name="clipping_attribute" type="text" value="null" 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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62 <param name="clipping_action" type="text" value="null" 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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63 <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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64 <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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65 <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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66 <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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67 <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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69 <expand macro="VS" />
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71 </inputs>
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72
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73 <outputs>
3
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74 <!-- here dataset discovery is based on fact that if OUTPUT_PER_RG=true this tool automatically adds .fastq extension to emitted files -->
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75 <data format="txt" name="report" label="SamToFastq run" hidden="true">
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76 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fastq" ext="fastqsanger" visible="true"/>
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77 </data>
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78 </outputs>
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80 <tests>
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81 <test>
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82 <param name="inputFile" value="picard_SamToFastq.bam" ftype="bam"/>
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83 <param name="output_per_rg" value="false"/>
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84 <param name="re_reverse" value="true"/>
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85 <param name="interleave" value="true"/>
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86 <param name="include_non_pf_reads" value="false"/>
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87 <param name="clipping_attribute" value="null" />
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88 <param name="clipping_action" value="null" />
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89 <param name="read1_trim" value="0" />
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90 <param name="read1_max_bases_to_write" value="-1"/>
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91 <param name="read2_trim" value="0" />
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92 <param name="read2_max_bases_to_write" value="-1"/>
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93 <param name="include_non_primary_alignments" value="false"/>
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94 <output name="report">
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95 <assert_contents>
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96 <has_line line="BAM" />
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97 </assert_contents>
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98 <discovered_dataset designation="INTERLEAVED" file="picard_SamToFastq_test1.fq" ftype="fastqsanger"/>
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99 </output>
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100 </test>
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101 </tests>
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102
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103 <stdio>
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104 <exit_code range="1:" level="fatal"/>
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105 </stdio>
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106
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107 <help>
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108
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109 **Purpose**
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110
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111 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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112
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113 -----
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114
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115 .. class:: warningmark
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116
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117 **DANGER: Multiple Outputs**
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118
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119 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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120
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121 @dataset_collections@
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122
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123 @description@
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124
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125 FASTQ=File
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126 F=File Output fastq file (single-end fastq or, if paired, first end of the pair fastq).
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127 Required. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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128
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129 SECOND_END_FASTQ=File
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130 F2=File Output fastq file (if paired, second end of the pair fastq). Default value: null.
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131 Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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132
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133 UNPAIRED_FASTQ=File
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134 FU=File Output fastq file for unpaired reads; may only be provided in paired-fastq mode Default
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135 value: null. Cannot be used in conjuction with option(s) OUTPUT_PER_RG (OPRG)
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136
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137 OUTPUT_PER_RG=Boolean
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138 OPRG=Boolean Output a fastq file per read group (two fastq files per read group if the group is
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139 paired). Default value: false. Possible values: {true, false} Cannot be used in
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140 conjuction with option(s) SECOND_END_FASTQ (F2) UNPAIRED_FASTQ (FU) FASTQ (F)
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141
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142 OUTPUT_DIR=File
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143 ODIR=File Directory in which to output the fastq file(s). Used only when OUTPUT_PER_RG is true.
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144 Default value: null.
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145
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146 RE_REVERSE=Boolean
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147 RC=Boolean Re-reverse bases and qualities of reads with negative strand flag set before writing them
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148 to fastq Default value: true. Possible values: {true, false}
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149
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150 INTERLEAVE=Boolean
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151 INTER=Boolean Will generate an interleaved fastq if paired, each line will have /1 or /2 to describe
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152 which end it came from Default value: false. Possible values: {true, false}
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153
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154 INCLUDE_NON_PF_READS=Boolean
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155 NON_PF=Boolean Include non-PF reads from the SAM file into the output FASTQ files. PF means 'passes
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156 filtering'. Reads whose 'not passing quality controls' flag is set are non-PF reads.
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157 Default value: false. Possible values: {true, false}
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158
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159 CLIPPING_ATTRIBUTE=String
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160 CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default
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161 value: null.
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162
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163 CLIPPING_ACTION=String
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164 CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities
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165 should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in
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166 the clipped region; and any integer means that the base qualities should be set to that
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167 value in the clipped region. Default value: null.
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168
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169 READ1_TRIM=Integer
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170 R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0.
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171
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172 READ1_MAX_BASES_TO_WRITE=Integer
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173 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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174 this many bases left after trimming, all will be written. If this value is null then all
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175 bases left after trimming will be written. Default value: null.
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176
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177 READ2_TRIM=Integer
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178 R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0.
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179
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180 READ2_MAX_BASES_TO_WRITE=Integer
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181 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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182 this many bases left after trimming, all will be written. If this value is null then all
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183 bases left after trimming will be written. Default value: null.
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184
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185 INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean
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186 If true, include non-primary alignments in the output. Support of non-primary alignments
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187 in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and
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188 there are paired reads with non-primary alignments. Default value: false.
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189 Possible values: {true, false}
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190
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191 @more_info@
0
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192
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193 </help>
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194 </tool>
3
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195
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196