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1 <tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0">
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2 <description>creates an unaligned BAM 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>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC
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6 -jar "\$JAVA_JAR_PATH/FastqToSam.jar"
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7 FASTQ="${input_fastq1}"
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8 #if str( $input_fastq2) != "None":
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9 FASTQ2="${input_fastq2}"
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10 #end if
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11 QUALITY_FORMAT="${ dict( fastqsanger='Standard', fastqcssanger='Standard', fastqillumina='Illumina', fastqsolexa='Solexa' )[ $input_fastq1.ext ] }" ##Solexa, Illumina, Standard
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12 OUTPUT="${output_bam}"
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13 READ_GROUP_NAME="${read_group_name}"
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14 SAMPLE_NAME="${sample_name}"
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15 #if $param_type.param_type_selector == "advanced":
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16 #if str( $param_type.library_name ) != "":
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17 LIBRARY_NAME="${param_type.library_name}"
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18 #end if
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19 #if str( $param_type.platform_unit ) != "":
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20 PLATFORM_UNIT="${param_type.platform_unit}"
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21 #end if
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22 #if str( $param_type.platform ) != "":
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23 PLATFORM="${param_type.platform}"
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24 #end if
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25 #if str( $param_type.sequencing_center ) != "":
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26 SEQUENCING_CENTER="${param_type.sequencing_center}"
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27 #end if
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28 #if str( $param_type.predicted_insert_size ) != "":
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29 PREDICTED_INSERT_SIZE="${param_type.predicted_insert_size}"
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30 #end if
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31 #if str( $param_type.description.value ) != "":
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32 DESCRIPTION="${param_type.description}"
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33 #end if
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34 #if str( $param_type.run_date ) != "":
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35 RUN_DATE="${param_type.run_date}"
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36 #end if
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37 #if str( $param_type.min_q ) != "":
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38 MIN_Q="${param_type.min_q}"
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39 #end if
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40 #if str( $param_type.min_q ) != "":
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41 MAX_Q="${param_type.max_q}"
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42 #end if
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43 SORT_ORDER="${param_type.sort_order}"
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44 #else:
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45 SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate
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46 #end if
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47 2>&1
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48 || echo "Error running Picard FastqToSAM" >&2
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49 </command>
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50 <inputs>
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51 <param name="input_fastq1" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ file" /> <!-- confirm that fastqcssanger also works -->
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52 <param name="input_fastq2" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" optional="True" label="Second FASTQ of paired end data" help="Only needed when using paired end data." >
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53 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
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54 <column name="name" index="0"/>
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55 <column name="value" index="0"/>
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56 <filter type="param_value" ref="input_fastq1" ref_attribute="ext" column="0"/>
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57 </options>
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58 </param>
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59 <param name="read_group_name" type="text" value="A" label="Read Group Name" />
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60 <param name="sample_name" type="text" value="unknown sample" label="Sample Name" />
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61 <conditional name="param_type">
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62 <param name="param_type_selector" type="select" label="Basic or Advanced options">
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63 <option value="basic" selected="True">Basic</option>
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64 <option value="advanced">Advanced</option>
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65 </param>
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66 <when value="basic">
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67 <!-- Do nothing here -->
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68 </when>
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69 <when value="advanced">
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70 <param name="library_name" type="text" value="" label="Library Name" />
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71 <param name="platform_unit" type="text" value="" label="Platform Unit" />
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72 <param name="platform" type="text" value="" label="Platform" />
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73 <param name="sequencing_center" type="text" value="" label="Sequencing Center" />
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74 <param name="predicted_insert_size" type="integer" value="" optional="True" label="Predicted Insert Size" />
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75 <param name="description" type="text" value="" label="Description" />
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76 <param name="run_date" type="text" value="" label="Run Date" />
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77 <param name="min_q" type="integer" optional="True" value="0" label="Min Q" />
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78 <param name="max_q" type="integer" optional="True" value="93" label="Max Q" />
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79 <param name="sort_order" type="select" label="Sort order">
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80 <option value="coordinate" selected="True">coordinate</option>
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81 <option value="queryname">queryname</option>
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82 <option value="unsorted">unsorted</option>
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83 </param>
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84 </when>
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85 </conditional>
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86 </inputs>
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87 <outputs>
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88 <data format="bam" name="output_bam" />
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89 </outputs>
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90 <tests>
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91 <test>
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92 <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
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93 <param name="input_fastq2" />
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94 <param name="read_group_name" value="A" />
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95 <param name="sample_name" value="unknown sample" />
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96 <param name="param_type_selector" value="basic" />
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97 <output name="output_bam" file="picard_fastq_to_sam_out1.bam" ftype="bam"/>
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98 </test>
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99 <test>
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100 <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
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101 <param name="input_fastq2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
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102 <param name="read_group_name" value="A" />
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103 <param name="sample_name" value="unknown sample" />
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104 <param name="param_type_selector" value="basic" />
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105 <output name="output_bam" file="picard_fastq_to_sam_out2.bam" ftype="bam"/>
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106 </test>
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107 </tests>
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108 <help>
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109 **What it does**
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110
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111 Picard: FastqToSam converts FASTQ files to unaligned BAM files.
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112
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113 ------
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114
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115 Please cite the website "http://picard.sourceforge.net".
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116
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117 ------
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118
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119
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120 **Input formats**
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121
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122 FastqToSam accepts FASTQ input files. If using paired-end data, you should select two FASTQ files.
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123
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124 ------
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125
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126 **Outputs**
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127
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128 The output is in BAM format, see http://samtools.sourceforge.net for more details.
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129
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130 -------
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131
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132 **FastqToSam settings**
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133
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134 This is list of FastqToSam options::
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135
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136 READ_GROUP_NAME=String Read group name Default value: A. This option can be set to 'null' to clear the default value.
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137 SAMPLE_NAME=String Sample name to insert into the read group header Required.
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138 LIBRARY_NAME=String The library name to place into the LB attribute in the read group header Default value: null.
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139 PLATFORM_UNIT=String The platform unit (often run_barcode.lane) to insert into the read group header Default value: null.
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140 PLATFORM=String The platform type (e.g. illumina, solid) to insert into the read group header Default value: null.
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141 SEQUENCING_CENTER=String The sequencing center from which the data originated Default value: null.
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142 PREDICTED_INSERT_SIZE=Integer Predicted median insert size, to insert into the read group header Default value: null.
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143 DESCRIPTION=String Inserted into the read group header Default value: null.
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144 </help>
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145 </tool>
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