|
4
|
1 <tool id="picard_FastqToSam" name="FASTQ to BAM / SAM" version="1.106.0">
|
|
|
2 <description>creates an unaligned BAM or SAM file</description>
|
|
|
3 <requirements><requirement type="package" version="1.106.0">picard</requirement></requirements>
|
|
|
4 <!-- Dan Blankenberg & dorine -->
|
|
|
5
|
|
|
6 <command interpreter="bash">fastq2sam_wrapper.sh
|
|
|
7 "${outputtype}"
|
|
|
8 "${output_bam}"
|
|
|
9 "${sample_name}"
|
|
|
10 "${read_group_name}"
|
|
|
11 FASTQ="${input_fastq1}"
|
|
|
12 #if str( $input_fastq2) != "None":
|
|
|
13 FASTQ2="${input_fastq2}"
|
|
|
14 #end if
|
|
|
15 QUALITY_FORMAT="${ dict( fastqsanger='Standard', fastqcssanger='Standard', fastqillumina='Illumina', fastqsolexa='Solexa' )[ $input_fastq1.ext ] }" ##Solexa, Illumina, Standard
|
|
|
16 #if $param_type.param_type_selector == "advanced":
|
|
|
17 #if str( $param_type.library_name ) != "":
|
|
|
18 LIBRARY_NAME="${param_type.library_name}"
|
|
|
19 #end if
|
|
|
20 #if str( $param_type.platform_unit ) != "":
|
|
|
21 PLATFORM_UNIT="${param_type.platform_unit}"
|
|
|
22 #end if
|
|
|
23 #if str( $param_type.platform ) != "":
|
|
|
24 PLATFORM="${param_type.platform}"
|
|
|
25 #end if
|
|
|
26 #if str( $param_type.sequencing_center ) != "":
|
|
|
27 SEQUENCING_CENTER="${param_type.sequencing_center}"
|
|
|
28 #end if
|
|
|
29 #if str( $param_type.predicted_insert_size ) != "":
|
|
|
30 PREDICTED_INSERT_SIZE="${param_type.predicted_insert_size}"
|
|
|
31 #end if
|
|
|
32 #if str( $param_type.description.value ) != "":
|
|
|
33 DESCRIPTION="${param_type.description}"
|
|
|
34 #end if
|
|
|
35 #if str( $param_type.run_date ) != "":
|
|
|
36 RUN_DATE="${param_type.run_date}"
|
|
|
37 #end if
|
|
|
38 #if str( $param_type.min_q ) != "":
|
|
|
39 MIN_Q="${param_type.min_q}"
|
|
|
40 #end if
|
|
|
41 #if str( $param_type.max_q ) != "":
|
|
|
42 MAX_Q="${param_type.max_q}"
|
|
|
43 #end if
|
|
|
44 SORT_ORDER="${param_type.sort_order}"
|
|
|
45 #else:
|
|
|
46 SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate
|
|
|
47 #end if
|
|
|
48 2>&1
|
|
|
49 || echo "Error running Picard FastqToSAM" >&2
|
|
|
50 </command>
|
|
|
51 <inputs>
|
|
|
52 <param name="input_fastq1" type="data" format="fastqsanger,fastqcsanger,fastqillumina,fastqsolexa" label="FASTQ file" />
|
|
|
53 <param name="input_fastq2" type="data" format="fastqsanger,fastqcsanger,fastqillumina,fastqsolexa" optional="True" label="Second FASTQ of paired end data" help="Only needed when using paired end data." >
|
|
|
54 <options options_filter_attribute="ext" from_parameter="tool.app.datatypes_registry.datatypes_by_extension" transform_lines="obj.keys()">
|
|
|
55 <column name="name" index="0"/>
|
|
|
56 <column name="value" index="0"/>
|
|
|
57 <filter type="param_value" ref="input_fastq1" ref_attribute="ext" column="0"/>
|
|
|
58 </options>
|
|
|
59 </param>
|
|
|
60 <param name="read_group_name" type="text" value="A" label="Read Group Name" />
|
|
|
61 <param name="sample_name" type="text" value="unknown_sample" label="Sample Name" />
|
|
|
62 <conditional name="param_type">
|
|
|
63 <param name="param_type_selector" type="select" label="Basic or Advanced options">
|
|
|
64 <option value="basic" selected="True">Basic</option>
|
|
|
65 <option value="advanced">Advanced</option>
|
|
|
66 </param>
|
|
|
67 <when value="basic">
|
|
|
68 <!-- Do nothing here -->
|
|
|
69 </when>
|
|
|
70 <when value="advanced">
|
|
|
71 <param name="library_name" type="text" value="" label="Library Name" />
|
|
|
72 <param name="platform_unit" type="text" value="" label="Platform Unit" />
|
|
|
73 <param name="platform" type="text" value="" label="Platform" />
|
|
|
74 <param name="sequencing_center" type="text" value="" label="Sequencing Center" />
|
|
|
75 <param name="predicted_insert_size" type="integer" value="" optional="True" label="Predicted Insert Size" />
|
|
|
76 <param name="description" type="text" value="" label="Description" />
|
|
|
77 <param name="run_date" type="text" value="" label="Run Date" />
|
|
|
78 <param name="min_q" type="integer" optional="True" value="0" label="Min Q" />
|
|
|
79 <param name="max_q" type="integer" optional="True" value="93" label="Max Q" />
|
|
|
80 <param name="sort_order" type="select" label="Sort order">
|
|
|
81 <option value="coordinate" selected="True">coordinate</option>
|
|
|
82 <option value="queryname">queryname</option>
|
|
|
83 <option value="unsorted">unsorted</option>
|
|
|
84 </param>
|
|
|
85 </when>
|
|
|
86 </conditional>
|
|
|
87 <param name="outputtype" type="select" label="Select the output format">
|
|
|
88 <option value="bam">bam</option>
|
|
|
89 <option value="sam">sam</option>
|
|
|
90 </param>
|
|
|
91 </inputs>
|
|
|
92 <outputs>
|
|
|
93 <data format="bam" name="output_bam" >
|
|
|
94 <change_format>
|
|
|
95 <when input="outputtype" value="sam" format="sam" />
|
|
|
96 </change_format>
|
|
|
97 </data>
|
|
|
98 </outputs>
|
|
|
99 <tests>
|
|
|
100 <test>
|
|
|
101 <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
|
|
|
102 <param name="input_fastq2" />
|
|
|
103 <param name="read_group_name" value="A" />
|
|
|
104 <param name="sample_name" value="unknown sample" />
|
|
|
105 <param name="param_type_selector" value="basic" />
|
|
|
106 <output name="output_bam" file="picard_fastq_to_sam_out1.bam" ftype="bam"/>
|
|
|
107 </test>
|
|
|
108 <test>
|
|
|
109 <param name="input_fastq1" value="bwa_wrapper_in2.fastqsanger" ftype="fastqsanger" />
|
|
|
110 <param name="input_fastq2" value="bwa_wrapper_in3.fastqsanger" ftype="fastqsanger" />
|
|
|
111 <param name="read_group_name" value="A" />
|
|
|
112 <param name="sample_name" value="unknown sample" />
|
|
|
113 <param name="param_type_selector" value="basic" />
|
|
|
114 <output name="output_bam" file="picard_fastq_to_sam_out2.bam" ftype="bam"/>
|
|
|
115 </test>
|
|
|
116 </tests>
|
|
|
117 <help>
|
|
|
118 **What it does**
|
|
|
119
|
|
|
120 Picard: FastqToSam converts FASTQ files to unaligned BAM files.
|
|
|
121
|
|
|
122 ------
|
|
|
123
|
|
|
124 Please cite the website "http://picard.sourceforge.net".
|
|
|
125
|
|
|
126 ------
|
|
|
127
|
|
|
128
|
|
|
129 **Input formats**
|
|
|
130
|
|
|
131 FastqToSam accepts FASTQ input files (note: the Fastq-sanger file format does not work with this Picard tool). If using paired-end data, you should select two FASTQ files.
|
|
|
132
|
|
|
133 ------
|
|
|
134
|
|
|
135 **Outputs**
|
|
|
136
|
|
|
137 The output is in BAM or in SAM format, see http://samtools.sourceforge.net for more details.
|
|
|
138
|
|
|
139 -------
|
|
|
140
|
|
|
141 **FastqToSam settings**
|
|
|
142
|
|
|
143 This is list of FastqToSam options::
|
|
|
144
|
|
|
145 READ_GROUP_NAME=String Read group name Default value: A. This option can be set to 'null' to clear the default value.
|
|
|
146 SAMPLE_NAME=String Sample name to insert into the read group header Required.
|
|
|
147 LIBRARY_NAME=String The library name to place into the LB attribute in the read group header Default value: null.
|
|
|
148 PLATFORM_UNIT=String The platform unit (often run_barcode.lane) to insert into the read group header Default value: null.
|
|
|
149 PLATFORM=String The platform type (e.g. illumina, solid) to insert into the read group header Default value: null.
|
|
|
150 SEQUENCING_CENTER=String The sequencing center from which the data originated Default value: null.
|
|
|
151 PREDICTED_INSERT_SIZE=Integer Predicted median insert size, to insert into the read group header Default value: null.
|
|
|
152 DESCRIPTION=String Inserted into the read group header Default value: null.
|
|
|
153 </help>
|
|
|
154 </tool>
|
