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comparison samtool_filter2.xml @ 0:2d4ae2f8231e draft

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Imported from capsule None
author devteam
date Thu, 27 Feb 2014 16:16:26 -0500
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children 94d5786febc4
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1 <tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.1">
2 <description>files on FLAG MAPQ RG LN or by region</description>
3 <requirements>
4 <requirement type="package" version="0.1.18">samtools</requirement>
5 </requirements>
6 <!--
7 samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-R rgFile] <in.bam>|<in.sam> [region1 [...]]
8 Usage: samtools view [options] <in.bam>|<in.sam> [region1 [...]]
9
10 Options: -b output BAM
11 -h print header for the SAM output
12 -H print header only (no alignments)
13 -S input is SAM
14 -u uncompressed BAM output (force -b)
15 -1 fast compression (force -b)
16 -x output FLAG in HEX (samtools-C specific)
17 -X output FLAG in string (samtools-C specific)
18 -c print only the count of matching records
19 -L FILE output alignments overlapping the input BED FILE [null]
20 -t FILE list of reference names and lengths (force -S) [null]
21 -T FILE reference sequence file (force -S) [null]
22 -o FILE output file name [stdout]
23 -R FILE list of read groups to be outputted [null]
24 -f INT required flag, 0 for unset [0]
25 -F INT filtering flag, 0 for unset [0]
26 -q INT minimum mapping quality [0]
27 -l STR only output reads in library STR [null]
28 -r STR only output reads in read group STR [null]
29 -? longer help
30 -->
31 <command>
32 ##set up input files, regions requires input.bam and input.bai
33 #if isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('bam').__class__):
34 #set $input = 'input.bam'
35 ln -s $input1 $input &amp;&amp;
36 ln -s $input1.metadata.bam_index input.bai &amp;&amp;
37 #elif isinstance($input1.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sam').__class__):
38 #set $input = 'input.sam'
39 ln -s $input1 $input &amp;&amp;
40 #end if
41 samtools view -o "$output1" $header
42
43 #if $input1.datatype.file_ext == 'sam':
44 -S
45 #end if
46
47 #if $outputtype.__str__ == "bam":
48 -b
49 #end if
50
51
52 #if $mapq.__str__ != '':
53 -q $mapq
54 #end if
55 #if $flag.filter.__str__ == 'yes':
56 #if $flag.reqBits.__str__ != 'None':
57 #set $reqs = $flag.reqBits.__str__.split(',')
58 #set $reqFlag = 0
59 #for $xn in $reqs:
60 #set $reqFlag += int(xn,16)
61 #end for
62 -f $hex($reqFlag)
63 #end if
64 #if $flag.skipBits.__str__ != 'None':
65 #set $skips = $flag.skipBits.__str__.split(',')
66 #set $skipFlag = 0
67 #for $xn in $skips:
68 #set $skipFlag += int(xn,16)
69 #end for
70 -F $hex($skipFlag)
71 #end if
72 #end if
73 #if $read_group.__str__.strip() != '':
74 -r $read_group
75 #end if
76 #if $library.__str__.strip() != '':
77 -l $library
78 #end if
79 #if $bed_file.__str__ != "None" and len($bed_file.__str__) > 0:
80 -L $bed_file
81 #end if
82 $input
83 #if $regions.__str__.strip() != '' and $input1.datatype.file_ext == 'bam':
84 $regions.__str__.strip()
85 #end if
86 ## need to redirect stderr message so galaxy does not think this failed
87 2>&amp;1
88 </command>
89 <inputs>
90 <param name="input1" type="data" format="sam,bam" label="SAM or BAM File to Filter" />
91 <param name="header" type="select" label="Header in output">
92 <option value="-h">Include Header</option>
93 <option value="">Exclude Header</option>
94 <option value="-H">Only the Header</option>
95 </param>
96 <param name="mapq" type="integer" value="" optional="true" label="Minimum MAPQ quality score">
97 <validator type="in_range" message="The MAPQ quality score can't be negative" min="0"/>
98 </param>
99 <conditional name="flag">
100 <param name="filter" type="select" label="Filter on bitwise flag">
101 <option value="no">no</option>
102 <option value="yes">yes</option>
103 </param>
104 <when value="no"/>
105 <when value="yes">
106 <param name="reqBits" type="select" multiple="true" display="checkboxes" label="Only output alignments with all of these flag bits set" >
107 <option value="0x0001">Read is paired</option>
108 <option value="0x0002">Read is mapped in a proper pair</option>
109 <option value="0x0004">The read is unmapped</option>
110 <option value="0x0008">The mate is unmapped</option>
111 <option value="0x0010">Read strand</option>
112 <option value="0x0020">Mate strand</option>
113 <option value="0x0040">Read is the first in a pair</option>
114 <option value="0x0080">Read is the second in a pair</option>
115 <option value="0x0100">The alignment or this read is not primary</option>
116 <option value="0x0200">The read fails platform/vendor quality checks</option>
117 <option value="0x0400">The read is a PCR or optical duplicate</option>
118 </param>
119 <param name="skipBits" type="select" multiple="true" display="checkboxes" label="Skip alignments with any of these flag bits set" >
120 <option value="0x0001">Read is paired</option>
121 <option value="0x0002">Read is mapped in a proper pair</option>
122 <option value="0x0004">The read is unmapped</option>
123 <option value="0x0008">The mate is unmapped</option>
124 <option value="0x0010">Read strand</option>
125 <option value="0x0020">Mate strand</option>
126 <option value="0x0040">Read is the first in a pair</option>
127 <option value="0x0080">Read is the second in a pair</option>
128 <option value="0x0100">The alignment or this read is not primary</option>
129 <option value="0x0200">The read fails platform/vendor quality checks</option>
130 <option value="0x0400">The read is a PCR or optical duplicate</option>
131 </param>
132 </when>
133 </conditional>
134 <param name="library" type="text" value="" size="20" label="Select alignments from Library"
135 help="Requires headers in the input SAM or BAM, otherwise no alignments will be output."/>
136 <param name="read_group" type="text" value="" size="20" label="Select alignments from Read Group"
137 help="Requires headers in the input SAM or BAM, otherwise no alignments will be output."/>
138 <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE"/>
139 <param name="regions" type="text" value="" size="180" label="Select regions (only used when the input is in BAM format)"
140 help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/>
141 <param name="outputtype" type="select" label="Select the output format">
142 <option value="bam">bam</option>
143 <option value="sam">sam</option>
144 </param>
145 </inputs>
146 <outputs>
147 <data name="output1" format_source="input1" label="${tool.name} on ${on_string}: ${input1.datatype.file_ext}">
148 <change_format>
149 <when input="outputtype" value="bam" format="bam" />
150 </change_format>
151 </data>
152 </outputs>
153 <tests>
154 <test>
155 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
156 <param name="header" value=""/>
157 <param name="filter" value="yes"/>
158 <param name="reqBits" value="0x0080"/>
159 <param name="outputtype" value="sam"/>
160 <output name="output1" >
161 <assert_contents>
162 <has_text text="141" />
163 <not_has_text text="77" />
164 </assert_contents>
165 </output>
166 </test>
167 <test>
168 <param name="input1" value="bam_to_sam_in2.sam" ftype="sam" />
169 <param name="header" value=""/>
170 <param name="filter" value="no"/>
171 <param name="read_group" value="rg1"/>
172 <param name="outputtype" value="sam"/>
173 <output name="output1" >
174 <assert_contents>
175 <has_text text="rg1" />
176 <not_has_text text="rg2" />
177 </assert_contents>
178 </output>
179 </test>
180 <test>
181 <param name="input1" value="bam_to_sam_in1.sam" ftype="sam" />
182 <param name="header" value=""/>
183 <param name="filter" value="yes"/>
184 <param name="skipBits" value="0x0008"/>
185 <param name="mapq" value="250"/>
186 <param name="outputtype" value="sam"/>
187 <output name="output1" >
188 <assert_contents>
189 <has_text text="both_reads_align_clip_marked" />
190 <not_has_text text="both_reads_present_only_first_aligns" />
191 </assert_contents>
192 </output>
193 </test>
194 </tests>
195 <help>
196
197
198 **What it does**
199
200 This tool uses the samtools view command in SAMTools_ toolkit to filter a SAM or BAM file on the MAPQ (mapping quality), FLAG bits, Read Group, Library, or region.
201
202 **Input**
203
204 Input is either a SAM or BAM file.
205
206 **Output**
207
208 The output file will be SAM or BAM (depending on the chosen option), filtered by the selected options.
209
210 **Options**
211
212 Filtering by read group or library requires headers in the input SAM or BAM file.
213
214 If regions are specified, only alignments overlapping the specified regions will be output. An alignment may be given multiple times if it is overlapping several regions.
215 A region can be presented, for example, in the following format::
216
217 chr2 (the whole chr2)
218 chr2:1000000 (region starting from 1,000,000bp)
219 chr2:1,000,000-2,000,000 (region between 1,000,000 and 2,000,000bp including the end points).
220
221 Note: The coordinate is 1-based.
222
223 Multiple regions may be specified, separated by a space character::
224
225 chr2:1000000-2000000 chr2:1,000,000-2,000,000 chrX
226
227
228
229 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
230
231 </help>
232 </tool>