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comparison picard_FastqToSam.xml @ 4:f4d018471628 draft default tip

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author jpruab
date Tue, 13 Aug 2013 12:09:14 -0400
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3:08b477977410 4:f4d018471628
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
40 #if str( $param_type.max_q ) != "":
41 MAX_Q="${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&gt;&amp;1
48 || echo "Error running Picard FastqToSAM" >&amp;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>