|
10
|
1 <tool id="samtools_slice_bam" name="Slice" version="2.0">
|
|
|
2 <description>BAM by genomic regions</description>
|
|
|
3 <macros>
|
|
|
4 <import>macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <!-- <code file="samtools_slice_options.py"/> -->
|
|
|
7 <expand macro="requirements"></expand>
|
|
|
8 <expand macro="stdio"></expand>
|
|
|
9 <expand macro="version_command"></expand>
|
|
|
10 <command>
|
|
|
11 <![CDATA[
|
|
|
12 ln -s "${input_bam}" temp_input.bam &&
|
|
|
13 ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai &&
|
|
|
14
|
|
|
15 #if str($slice_method.slice_method_selector) == "bed":
|
|
|
16
|
|
|
17 samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam &&
|
|
|
18
|
|
|
19 #elif str($slice_method.slice_method_selector) == "chr":
|
|
|
20
|
|
|
21 samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
|
|
|
22 ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } &&
|
|
|
23
|
|
|
24 #elif str($slice_method.slice_method_selector) == "man":
|
|
|
25
|
|
|
26 samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam
|
|
|
27
|
|
|
28 #for $region in $slice_method.regions:
|
|
|
29 "${region.chrom}:${region.start}-${region.end}"
|
|
|
30 #end for
|
|
|
31
|
|
|
32 &&
|
|
|
33
|
|
|
34 #end if
|
|
|
35
|
|
|
36 samtools sort -O bam -T sorted -@ \${GALAXY_SLOTS:-1} -o "${output_bam}" unsorted_output.bam
|
|
|
37 ]]>
|
|
|
38 </command>
|
|
|
39 <inputs>
|
|
|
40 <param name="input_bam" format="bam" label="Select BAM dataset to slice" type="data" />
|
|
|
41 <conditional name="slice_method">
|
|
|
42 <param name="slice_method_selector" type="select" label="How do you want to slice your dataset?">
|
|
|
43 <option value="bed">using a list of intervals from a BED dataset</option>
|
|
|
44 <option value="chr">by chromosomes/contigs present in the BAM dataset</option>
|
|
|
45 <option value="man">by chromosomes/contigs and coordinates</option>
|
|
|
46 </param>
|
|
|
47 <when value="bed">
|
|
|
48 <param format="bed" label="BED file" name="input_interval" type="data" help="BED datasets can be obtained using "Get Data -> UCSC Main" datasource."/>
|
|
|
49 </when>
|
|
|
50 <when value="chr">
|
|
|
51 <param name="refs" type="select" optional="False" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Click and type in the box above to see options. You can select multiple entries. If "No options available" is displayed, you need to re-detect metadata on the input dataset. See help section below.">
|
|
|
52
|
|
|
53 <!-- The options tagset below extracts reference names from bam file metadata -->
|
|
|
54 <!-- This will not work with bed files with old style metadata. However this -->
|
|
|
55 <!-- Can be easily fixed by re-deceting metadata on a bam dataset by clicking -->
|
|
|
56 <!-- The pencil icon and settind datatype to "bam" -->
|
|
|
57 <!-- This change has been commited in the following pull request: -->
|
|
|
58 <!-- https://github.com/galaxyproject/galaxy/pull/107 -->
|
|
|
59
|
|
|
60 <options>
|
|
|
61 <filter type="data_meta" ref="input_bam" key="reference_names" />
|
|
|
62 </options>
|
|
|
63 </param>
|
|
|
64 </when>
|
|
|
65 <when value="man">
|
|
|
66 <repeat name="regions" title="Regions" min="1">
|
|
|
67 <param name="chrom" type="select" optional="False" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Select chromosome/contig from the list. If "No options available" is displayed, you need to re-detect metadata on the input dataset. See help section below.">
|
|
|
68
|
|
|
69 <!-- See comments above -->
|
|
|
70
|
|
|
71 <options>
|
|
|
72 <filter type="data_meta" ref="input_bam" key="reference_names" />
|
|
|
73 </options>
|
|
|
74 </param>
|
|
|
75 <param name="start" type="integer" min="1" value="0" label="Enter START coordinate (1-based)"/>
|
|
|
76 <param name="end" type="integer" min="1" value="100" label="Enter END coordinate"/>
|
|
|
77 </repeat>
|
|
|
78
|
|
|
79
|
|
|
80 </when>
|
|
|
81 </conditional>
|
|
|
82
|
|
|
83 </inputs>
|
|
|
84 <outputs>
|
|
|
85 <data format="bam" name="output_bam" />
|
|
|
86 </outputs>
|
|
|
87 <tests>
|
|
|
88 <test>
|
|
|
89 <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
|
|
|
90 <param name="slice_method_selector" value="bed"/>
|
|
|
91 <param ftype="bed" name="input_interval" value="bam-slice.bed" />
|
|
|
92 <output file="bam-slice-test1.bam" ftype="bam" name="output_bam" />
|
|
|
93 </test>
|
|
|
94 <test>
|
|
|
95 <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
|
|
|
96 <param name="slice_method_selector" value="chr"/>
|
|
|
97 <param name="refs" value="chrM" />
|
|
|
98 <output file="bam-slice-test2.bam" ftype="bam" name="output_bam" />
|
|
|
99 </test>
|
|
|
100 <test>
|
|
|
101 <param ftype="bam" name="input_bam" value="bam-slice-input.bam" />
|
|
|
102 <param name="slice_method_selector" value="man"/>
|
|
|
103 <param name="chrom" value="chrM" />
|
|
|
104 <param name="start" value="1" />
|
|
|
105 <param name="end" value="1000" />
|
|
|
106 <output file="bam-slice-test3.bam" ftype="bam" name="output_bam" />
|
|
|
107 </test>
|
|
|
108 </tests>
|
|
|
109 <help>
|
|
|
110 <![CDATA[
|
|
|
111
|
|
|
112 **What it does**
|
|
|
113
|
|
|
114 Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates. BED datasets can be obtained from **Get Data -> UCSC Main**.
|
|
|
115
|
|
|
116 This tool is based on ``samtools view`` command.
|
|
|
117
|
|
|
118 @no-chrom-options@
|
|
|
119
|
|
|
120 ]]>
|
|
|
121 </help>
|
|
|
122 <expand macro="citations"></expand>
|
|
|
123 </tool>
|
