|
0
|
1 <tool id="samtools_bam2fq" name="Convert BAM to FASTQ" version="0.0.2">
|
|
|
2 <description>samtools bam2fq</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="binary">samtools</requirement>
|
|
|
5 <requirement type="package" version="1.1">samtools</requirement>
|
|
|
6 </requirements>
|
|
|
7 <version_command>samtools 2>&1 | grep -i "Version:"</version_command>
|
|
|
8 <command>
|
|
|
9 #if $action_mode.mode == "pairs":
|
|
|
10 ## Sort by name for pair-aware output (should give nice interlaced FASTQ)
|
|
|
11 ## Galaxy has a tendancy to automatically apply co-ordindate sorting,
|
|
|
12 ## so just do this every time. If it was name sorted, pay an IO overhead.
|
|
|
13 ## Note requiring -T is samtools issue 295
|
|
|
14 samtools sort -n -O bam -T TEMP_SORT "$input_bam" | samtools bam2fq -s "$singletons_fastq" - > "$pairs_fastq"
|
|
|
15 #else
|
|
|
16 ## Naive conversion using order in the input file
|
|
|
17 samtools bam2fq $suffices $orig_qual "$input_bam" > "$out_fastq"
|
|
|
18 #end if
|
|
|
19 </command>
|
|
|
20 <inputs>
|
|
|
21 <!-- Unlike samtools 0.1.x, samtools 1.1 will autodetect SAM vs BAM -->
|
|
|
22 <param name="input_bam" type="data" format="bam,sam" label="Input SAM/BAM file" />
|
|
|
23 <param name="suffices" type="boolean" label="Add /1 and /2 suffices to paired reads?"
|
|
|
24 truevalue="" falsevalue="-n" checked="true" />
|
|
|
25 <param name="orig_qual" type="boolean" label="Use original qualities (OQ tags) if present?"
|
|
|
26 truevalue="-O" falsevalue="" checked="false" />
|
|
|
27 <!-- Using a condition here to allow different output files; default to paired mode -->
|
|
|
28 <conditional name="action_mode">
|
|
|
29 <param name="mode" type="select" label="Mode of action">
|
|
|
30 <option value="pairs" selected="true">Sort by name, then divide into paired and singletons (two FASTQ files)</option>
|
|
|
31 <option value="naive">No pre-sorting, all reads in a single FASTQ file</option>
|
|
|
32 </param>
|
|
|
33 </conditional>
|
|
|
34 </inputs>
|
|
|
35 <outputs>
|
|
|
36 <data name="pairs_fastq" format="fastqsanger" label="$input_bam.name (bam2fq pairs)">
|
|
|
37 <filter>(action_mode['mode'] == 'pairs')</filter>
|
|
|
38 </data>
|
|
|
39 <data name="singletons_fastq" format="fastqsanger" label="$input_bam.name (bam2fq singletons)">
|
|
|
40 <filter>(action_mode['mode'] == 'pairs')</filter>
|
|
|
41 </data>
|
|
|
42 <data name="out_fastq" format="fastqsanger" label="$input_bam.name (bam2fq)">
|
|
|
43 <filter>(action_mode['mode'] == 'naive')</filter>
|
|
|
44 </data>
|
|
|
45 </outputs>
|
|
|
46 <stdio>
|
|
|
47 <!-- Assume anything other than zero is an error -->
|
|
|
48 <exit_code range="1:" />
|
|
|
49 <exit_code range=":-1" />
|
|
|
50 </stdio>
|
|
|
51 <tests>
|
|
|
52 <test>
|
|
|
53 <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
|
|
|
54 <param name="suffices" value="true" />
|
|
|
55 <param name="orig_qual" value="false" />
|
|
|
56 <param name="mode" value="naive" />
|
|
|
57 <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
|
|
|
58 </test>
|
|
|
59 <test>
|
|
|
60 <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
|
|
|
61 <param name="suffices" value="true" />
|
|
|
62 <param name="orig_qual" value="true" />
|
|
|
63 <param name="mode" value="naive" />
|
|
|
64 <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
|
|
|
65 </test>
|
|
|
66 <test>
|
|
|
67 <param name="input_bam" value="sam_spec_padded.sam" ftype="sam" />
|
|
|
68 <param name="mode" value="naive" />
|
|
|
69 <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
|
|
|
70 </test>
|
|
|
71 <test>
|
|
|
72 <param name="input_bam" value="sam_spec_padded.depad.bam" ftype="bam" />
|
|
|
73 <param name="mode" value="naive" />
|
|
|
74 <output name="out_fastq" file="sam_spec_padded.bam2fq.fastq" ftype="fastqsanger" />
|
|
|
75 </test>
|
|
|
76 <test>
|
|
|
77 <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
|
|
|
78 <param name="suffices" value="false"/>
|
|
|
79 <param name="mode" value="naive" />
|
|
|
80 <output name="out_fastq" file="sam_spec_padded.bam2fq_no_suf.fastq" ftype="fastqsanger" />
|
|
|
81 </test>
|
|
|
82 <test>
|
|
|
83 <param name="input_bam" value="sam_spec_padded.bam" ftype="bam" />
|
|
|
84 <param name="suffices" value="true" />
|
|
|
85 <param name="orig_qual" value="false" />
|
|
|
86 <param name="mode" value="pairs" />
|
|
|
87 <output name="pairs_fastq" file="sam_spec_padded.bam2fq_pairs.fastq" ftype="fastqsanger" />
|
|
|
88 <output name="singletons_fastq" file="sam_spec_padded.bam2fq_singles.fastq" ftype="fastqsanger" />
|
|
|
89 </test>
|
|
|
90 <test>
|
|
|
91 <param name="input_bam" value="sam_spec_padded.sam" ftype="sam" />
|
|
|
92 <param name="suffices" value="true" />
|
|
|
93 <param name="orig_qual" value="false" />
|
|
|
94 <param name="mode" value="pairs" />
|
|
|
95 <output name="pairs_fastq" file="sam_spec_padded.bam2fq_pairs.fastq" ftype="fastqsanger" />
|
|
|
96 <output name="singletons_fastq" file="sam_spec_padded.bam2fq_singles.fastq" ftype="fastqsanger" />
|
|
|
97 </test>
|
|
|
98 </tests>
|
|
|
99 <help>
|
|
|
100 **What it does**
|
|
|
101
|
|
|
102 This tool runs the ``samtools bam2fq`` command in the SAMtools toolkit.
|
|
|
103
|
|
|
104 By default this will pre-sort your SAM/BAM file by read name and split your
|
|
|
105 reads into an interlaced FASTQ file for paired reads, and a separate FASTQ
|
|
|
106 file for singleton reads. A naive conversion is also offered which gives a
|
|
|
107 single FASTQ file with the reads ordered as in the input SAM/BAM file.
|
|
|
108
|
|
|
109 It is quite common to wish to remap high-throughput sequencing data. If you
|
|
|
110 only have the mapped reads in SAM/BAM format, this tool can "unmap" them to
|
|
|
111 recover FASTQ format reads to input into an alternative mapping tool.
|
|
|
112
|
|
|
113 BAM files can hold both aligned reads and unaligned reads, so another example
|
|
|
114 usage would be to filter your BAM file to get only the unaligned reads, and
|
|
|
115 turn those back in FASTQ using this tool ready for *de novo* assembly, or to
|
|
|
116 try mapping against another reference sequence.
|
|
|
117
|
|
|
118
|
|
|
119 **Citation**
|
|
|
120
|
|
|
121 If you use this Galaxy tool in work leading to a scientific publication please
|
|
|
122 cite:
|
|
|
123
|
|
|
124 Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools.
|
|
|
125 Bioinformatics 25(16), 2078-9.
|
|
|
126 http://dx.doi.org/10.1093/bioinformatics/btp352
|
|
|
127
|
|
|
128 Peter J.A. Cock (2014), Galaxy wrapper for the samtools bam2fq command
|
|
|
129 http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq
|
|
|
130
|
|
|
131 This wrapper is available to install into other Galaxy Instances via the Galaxy
|
|
|
132 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_bam2fq
|
|
|
133 </help>
|
|
|
134 <citations>
|
|
|
135 <citation type="doi">10.1093/bioinformatics/btp352</citation>
|
|
|
136 </citations>
|
|
|
137 </tool>
|
