Mercurial > repos > devteam > picard
annotate picard_FastqToSam.xml @ 3:bf1c3f9f8282
Fix for FastqToSam MAX_Q usage detection.
| author | Daniel Blankenberg <dan@bx.psu.edu> |
|---|---|
| date | Fri, 03 May 2013 17:13:01 -0400 |
| parents | 1cd7f3b42609 |
| children | 3d4f1fa26f0e |
| rev | line source |
|---|---|
| 0 | 1 <tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0"> |
| 2 <description>creates an unaligned BAM file</description> | |
| 3 <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> | |
| 4 <!-- Dan Blankenberg --> | |
| 5 <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC | |
| 6 -jar "\$JAVA_JAR_PATH/FastqToSam.jar" | |
| 7 FASTQ="${input_fastq1}" | |
| 8 #if str( $input_fastq2) != "None": | |
| 9 FASTQ2="${input_fastq2}" | |
| 10 #end if | |
| 11 QUALITY_FORMAT="${ dict( fastqsanger='Standard', fastqcssanger='Standard', fastqillumina='Illumina', fastqsolexa='Solexa' )[ $input_fastq1.ext ] }" ##Solexa, Illumina, Standard | |
| 12 OUTPUT="${output_bam}" | |
| 13 READ_GROUP_NAME="${read_group_name}" | |
| 14 SAMPLE_NAME="${sample_name}" | |
| 15 #if $param_type.param_type_selector == "advanced": | |
| 16 #if str( $param_type.library_name ) != "": | |
| 17 LIBRARY_NAME="${param_type.library_name}" | |
| 18 #end if | |
| 19 #if str( $param_type.platform_unit ) != "": | |
| 20 PLATFORM_UNIT="${param_type.platform_unit}" | |
| 21 #end if | |
| 22 #if str( $param_type.platform ) != "": | |
| 23 PLATFORM="${param_type.platform}" | |
| 24 #end if | |
| 25 #if str( $param_type.sequencing_center ) != "": | |
| 26 SEQUENCING_CENTER="${param_type.sequencing_center}" | |
| 27 #end if | |
| 28 #if str( $param_type.predicted_insert_size ) != "": | |
| 29 PREDICTED_INSERT_SIZE="${param_type.predicted_insert_size}" | |
| 30 #end if | |
| 31 #if str( $param_type.description.value ) != "": | |
| 32 DESCRIPTION="${param_type.description}" | |
| 33 #end if | |
| 34 #if str( $param_type.run_date ) != "": | |
| 35 RUN_DATE="${param_type.run_date}" | |
| 36 #end if | |
| 37 #if str( $param_type.min_q ) != "": | |
| 38 MIN_Q="${param_type.min_q}" | |
| 39 #end if | |
|
3
bf1c3f9f8282
Fix for FastqToSam MAX_Q usage detection.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
0
diff
changeset
|
40 #if str( $param_type.max_q ) != "": |
| 0 | 41 MAX_Q="${param_type.max_q}" |
| 42 #end if | |
| 43 SORT_ORDER="${param_type.sort_order}" | |
| 44 #else: | |
| 45 SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate | |
| 46 #end if | |
| 47 2>&1 | |
| 48 || echo "Error running Picard FastqToSAM" >&2 | |
| 49 </command> | |
| 50 <inputs> | |
| 51 <param name="input_fastq1" type="data" format="fastqsanger,fastqillumina,fastqsolexa,fastqcssanger" label="FASTQ file" /> <!-- confirm that fastqcssanger also works --> | |
| 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." > | |
| 53 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()"> | |
| 54 <column name="name" index="0"/> | |
| 55 <column name="value" index="0"/> | |
| 56 <filter type="param_value" ref="input_fastq1" ref_attribute="ext" column="0"/> | |
| 57 </options> | |
| 58 </param> | |
| 59 <param name="read_group_name" type="text" value="A" label="Read Group Name" /> | |
| 60 <param name="sample_name" type="text" value="unknown sample" label="Sample Name" /> | |
| 61 <conditional name="param_type"> | |
| 62 <param name="param_type_selector" type="select" label="Basic or Advanced options"> | |
| 63 <option value="basic" selected="True">Basic</option> | |
| 64 <option value="advanced">Advanced</option> | |
| 65 </param> | |
| 66 <when value="basic"> | |
| 67 <!-- Do nothing here --> | |
| 68 </when> | |
| 69 <when value="advanced"> | |
| 70 <param name="library_name" type="text" value="" label="Library Name" /> | |
| 71 <param name="platform_unit" type="text" value="" label="Platform Unit" /> | |
| 72 <param name="platform" type="text" value="" label="Platform" /> | |
| 73 <param name="sequencing_center" type="text" value="" label="Sequencing Center" /> | |
| 74 <param name="predicted_insert_size" type="integer" value="" optional="True" label="Predicted Insert Size" /> | |
| 75 <param name="description" type="text" value="" label="Description" /> | |
| 76 <param name="run_date" type="text" value="" label="Run Date" /> | |
| 77 <param name="min_q" type="integer" optional="True" value="0" label="Min Q" /> | |
| 78 <param name="max_q" type="integer" optional="True" value="93" label="Max Q" /> | |
| 79 <param name="sort_order" type="select" label="Sort order"> | |
| 80 <option value="coordinate" selected="True">coordinate</option> | |
| 81 <option value="queryname">queryname</option> | |
| 82 <option value="unsorted">unsorted</option> | |
| 83 </param> | |
| 84 </when> | |
| 85 </conditional> | |
| 86 </inputs> | |
| 87 <outputs> | |
| 88 <data format="bam" name="output_bam" /> | |
| 89 </outputs> | |
| 90 <tests> | |
| 91 <test> | |
| 92 <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /> | |
| 93 <param name="input_fastq2" /> | |
| 94 <param name="read_group_name" value="A" /> | |
| 95 <param name="sample_name" value="unknown sample" /> | |
| 96 <param name="param_type_selector" value="basic" /> | |
| 97 <output name="output_bam" file="picard_fastq_to_sam_out1.bam" ftype="bam"/> | |
| 98 </test> | |
| 99 <test> | |
| 100 <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" /> | |
| 101 <param name="input_fastq2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" /> | |
| 102 <param name="read_group_name" value="A" /> | |
| 103 <param name="sample_name" value="unknown sample" /> | |
| 104 <param name="param_type_selector" value="basic" /> | |
| 105 <output name="output_bam" file="picard_fastq_to_sam_out2.bam" ftype="bam"/> | |
| 106 </test> | |
| 107 </tests> | |
| 108 <help> | |
| 109 **What it does** | |
| 110 | |
| 111 Picard: FastqToSam converts FASTQ files to unaligned BAM files. | |
| 112 | |
| 113 ------ | |
| 114 | |
| 115 Please cite the website "http://picard.sourceforge.net". | |
| 116 | |
| 117 ------ | |
| 118 | |
| 119 | |
| 120 **Input formats** | |
| 121 | |
| 122 FastqToSam accepts FASTQ input files. If using paired-end data, you should select two FASTQ files. | |
| 123 | |
| 124 ------ | |
| 125 | |
| 126 **Outputs** | |
| 127 | |
| 128 The output is in BAM format, see http://samtools.sourceforge.net for more details. | |
| 129 | |
| 130 ------- | |
| 131 | |
| 132 **FastqToSam settings** | |
| 133 | |
| 134 This is list of FastqToSam options:: | |
| 135 | |
| 136 READ_GROUP_NAME=String Read group name Default value: A. This option can be set to 'null' to clear the default value. | |
| 137 SAMPLE_NAME=String Sample name to insert into the read group header Required. | |
| 138 LIBRARY_NAME=String The library name to place into the LB attribute in the read group header Default value: null. | |
| 139 PLATFORM_UNIT=String The platform unit (often run_barcode.lane) to insert into the read group header Default value: null. | |
| 140 PLATFORM=String The platform type (e.g. illumina, solid) to insert into the read group header Default value: null. | |
| 141 SEQUENCING_CENTER=String The sequencing center from which the data originated Default value: null. | |
| 142 PREDICTED_INSERT_SIZE=Integer Predicted median insert size, to insert into the read group header Default value: null. | |
| 143 DESCRIPTION=String Inserted into the read group header Default value: null. | |
| 144 </help> | |
| 145 </tool> |