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1 <tool name="FastqToSam" id="picard_FastqToSam" version="1.126.0">
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2 <description>convert Fastq data into unaligned BAM</description>
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3 <requirements>
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4 <requirement type="package" version="1.126.0">picard</requirement>
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5 </requirements>
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6
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7 <macros>
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8 <import>picard_macros.xml</import>
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9 </macros>
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10
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11 <command>
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12 @java_options@
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13
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14 java -jar \$JAVA_JAR_PATH/picard.jar
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15 FastqToSam
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16
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17 #if str( $input_type.input_type_selector ) == "se":
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18 FASTQ="${input_type.fastq}"
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19 #elif str( $input_type.input_type_selector ) == "pe":
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20 FASTQ="${input_type.fastq}"
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21 FASTQ2="${input_type.fastq2}"
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22 #else
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23 FASTQ="${input_type.fastq.forward}"
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24 FASTQ2="${input_type.fastq.reverse}"
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25 #end if
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26
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27 QUALITY_FORMAT="${quality_format}"
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28 OUTPUT="${outFile}"
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29 READ_GROUP_NAME="${read_group_name}"
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30 SAMPLE_NAME="${sample_name}"
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31
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32 #if str( $library_name ):
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33 LIBRARY_NAME="${library_name}"
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34 #end if
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35
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36 #if str( $platform_unit ):
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37 PLATFORM_UNIT="${platform_unit}"
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38 #end if
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39
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40 #if str( $platform ):
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41 PLATFORM="${platform}"
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42 #end if
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43
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44 #if str( $sequencing_center ):
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45 SEQUENCING_CENTER="${sequencing_center}"
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46 #end if
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47
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48 #if str( $predicted_insert_size ):
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49 PREDICTED_INSERT_SIZE="${predicted_insert_size}"
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50 #end if
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51
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52 #if str( $comment ):
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53 COMMENT="${comment}"
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54 #end if
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55
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56 #if str( $description ):
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57 DESCRIPTION="${description}"
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58 #end if
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59
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60 #if str( $run_date ):
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61 RUN_DATE="${run_date}"
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62 #end if
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63
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64 MIN_Q="${min_q}"
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65 MAX_Q="${max_q}"
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66 STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}"
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67 ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}"
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68
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69 SORT_ORDER=coordinate
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70 VALIDATION_STRINGENCY="${validation_stringency}"
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71 QUIET=true
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72 VERBOSITY=ERROR
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73
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74 </command>
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75 <inputs>
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76 <conditional name="input_type">
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77 <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
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78 <option value="se">Single end (single dataset)</option>
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79 <option value="pe">Paired end (two datasets)</option>
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80 <option value="pc">Paired collection</option>
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81 </param>
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82 <when value="se">
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83 <param name="fastq" type="data" format="fastq" label="Input fastq file for single end data" help="FASTQ"/>
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84 </when>
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85 <when value="pe">
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86 <param name="fastq" type="data" format="fastq" label="Input fastq file for the first read in paired end data" help="FASTQ"/>
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87 <param name="fastq2" type="data" format="fastq" label="Input fastq file for the second read of paired end data" help="FASTQ2"/>
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88 </when>
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89 <when value="pc">
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90 <param name="fastq" type="data_collection" collection_type="paired" label="FASTQ paired dataset collection" help="FASTQ and FASTQ2; A collection of two datasets with forward and reverse reads. See help below on explanation of dataset collections"/>
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91 </when>
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92 </conditional>
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93
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94 <param name="quality_format" type="select" label="Select quality encoding scheme" help="QUALITY_FORMAT">
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95 <option value="Standard" selected="True">Sanger (+33)</option>
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96 <option value="Illumina">Illumina (+64)</option>
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97 <option value="Solexa">Solexa (+66)</option>
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98 </param>
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99
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100 <param name="read_group_name" type="text" size="20" value="A" label="Read group name" help="READ_GROUP_NAME"/>
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101 <param name="sample_name" type="text" size="20" value="sample-a" label="Sample name" help="SAMPLE_NAME"/>
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102 <param name="library_name" type="text" size="20" optional="True" label="The library name" help="LIBRARY_NAME; Optional"/>
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103 <param name="platform_unit" type="text" size="20" optional="True" label="The platform unit (often run_barcode.lane)" help="PLATFORM_UNIT; Optional"/>
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104 <param name="platform" type="text" size="20" optional="True" label="The platform type (e.g. illumina, 454)" help="PLATFORM; Optional"/>
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105 <param name="sequencing_center" type="text" size="20" optional="True" label="The sequencing center from which the data originated" help="SEQUENCING_CENTER; Optional"/>
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106
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107 <param name="predicted_insert_size" type="integer" min="0" max="100000" optional="True" label="Predicted median insert size, to insert into the read group header" help="PREDICTED_INSERT_SIZE; Optional"/>
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108 <param name="comment" type="text" size="20" optional="True" label="Comment to include in the output dataset's header" help="COMMENT; Optional"/>
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109 <param name="description" type="text" size="20" optional="True" label="Optional description information" help="DESCRIPTION; Optional"/>
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110 <param name="run_date" optional="True" type="text" label="Run date" help="RGDT; Optional; Format=YYYY-MM-DD (eg 1997-07-16)"/>
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111 <param name="min_q" type="integer" value="0" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MIN_Q; An exception will be thrown if a quality is less than this value; default=0"/>
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112 <param name="max_q" type="integer" value="93" min="0" max="100" label="Minimum quality allowed in the input fastq" help="MAX_Q; An exception will be thrown if a quality is greater than this value; default=93"/>
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113 <param name="strip_unpairied_mate_number" type="boolean" truevalue="true" falsevalue="false" label="If true and this is an unpaired fastq any occurance of '/1' will be removed from the end of a read name" help="STRIP_UNPAIRED_MATE_NUMBER; default=false"/>
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114 <param name="allow_and_ignore_empty_lines" type="boolean" truevalue="true" falsevalue="false" label="Allow (and ignore) empty lines" help="ALLOW_AND_IGNORE_EMPTY_LINES; default=false"/>
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115
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116 <expand macro="VS" />
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117
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118 </inputs>
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119
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120 <outputs>
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121 <data format="bam" name="outFile" label="${tool.name} on ${on_string}: reads as unaligned BAM"/>
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122 </outputs>
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123
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124 <tests>
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125 <test>
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126 <param name="input_type_selector" value="pe" />
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127 <param name="quality_format" value="Standard" />
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128 <param name="read_group_name" value="A" />
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129 <param name="sample_name" value="sample-a" />
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130 <param name="library_name" value="A"/>
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131 <param name="platform_unit" value="A"/>
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132 <param name="platform" value="Illumina"/>
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133 <param name="sequencing_center" value="A"/>
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134 <param name="predicted_insert_size" value="300"/>
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135 <param name="comment" value="A"/>
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136 <param name="description" value="A"/>
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137 <param name="run_date" value="2014-10-10"/>
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138 <param name="min_q" value="0" />
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139 <param name="max_q" value="93" />
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140 <param name="strip_unpairied_mate_number" value="False" />
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141 <param name="allow_and_ignore_empty_lines" value="False" />
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142 <param name="validation_stringency" value="LENIENT"/>
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143 <param name="fastq" value="picard_FastqToSam_read1.fq" ftype="fastq" />
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144 <param name="fastq2" value="picard_FastqToSam_read2.fq" ftype="fastq" />
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145 <output name="outFile" file="picard_FastqToSam_test1.bam" ftype="bam" lines_diff="4"/>
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146 </test>
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147 </tests>
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148
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149 <stdio>
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150 <exit_code range="1:" level="fatal"/>
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151 </stdio>
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152
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153 <help>
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154
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155 .. class:: infomark
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156
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157 **Purpose**
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158
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159 Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
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160
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161 @dataset_collections@
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162
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163 @RG@
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164
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165 @description@
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166
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167 FASTQ=File
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168 F1=File Input fastq file for single end data, or first read in paired end
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169 data. Required.
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170
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171 FASTQ2=File
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172 F2=File Input fastq file for the second read of paired end data (if used).
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173
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174 QUALITY_FORMAT=FastqQualityFormat
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175 V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either Solexa for
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176 pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above
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177 (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33.
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178 If this value is not specified, the quality format will be detected automatically.
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179 Default value: null. Possible values: {Solexa, Illumina, Standard}
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180
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181 READ_GROUP_NAME=String
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182 RG=String Read group name Default value: A.
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183
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184 SAMPLE_NAME=String
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185 SM=String Sample name to insert into the read group header Required.
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186
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187 LIBRARY_NAME=String
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188 LB=String The library name to place into the LB attribute in the read group header.
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189
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190 PLATFORM_UNIT=String
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191 PU=String The platform unit (often run_barcode.lane) to insert into the read group header.
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192
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193 PLATFORM=String
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194 PL=String The platform type (e.g. illumina, solid) to insert into the read group header.
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195
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196 SEQUENCING_CENTER=String
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197 CN=String The sequencing center from which the data originated.
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198
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199 PREDICTED_INSERT_SIZE=Integer
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200 PI=Integer Predicted median insert size, to insert into the read group header.
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201
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202 COMMENT=String
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203 CO=String Comment to include in the merged output file's header.
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204
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205 DESCRIPTION=String
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206 DS=String Inserted into the read group header.
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207
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208 RUN_DATE=Iso8601Date
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209 DT=Iso8601Date Date the run was produced, to insert into the read group header.
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210
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211 MIN_Q=Integer Minimum quality allowed in the input fastq. An exception will be thrown if a quality is
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212 less than this value. Default value: 0.
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213
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214 MAX_Q=Integer Maximum quality allowed in the input fastq. An exception will be thrown if a quality is
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215 greater than this value. Default value: 93.
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216
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217 STRIP_UNPAIRED_MATE_NUMBER=Boolean
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218 If true and this is an unpaired fastq any occurance of '/1' will be removed from the end
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219 of a read name. Default value: false. Possible values: {true, false}
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220
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221 ALLOW_AND_IGNORE_EMPTY_LINES=Boolean
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222 Allow (and ignore) empty lines Default value: false. Possible values: {true, false}
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223
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224
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225 @more_info@
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226
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227 </help>
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228 </tool>
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229
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230
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