Mercurial > repos > brenninc > samtools_flag_filter_1_2
comparison samtools_flag_filter.xml @ 0:97bb72be07f9 draft default tip
Uploaded first version
author | brenninc |
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date | Tue, 10 May 2016 03:59:17 -0400 |
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-1:000000000000 | 0:97bb72be07f9 |
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1 <tool id="samtools_flag_filter" name="Samtools flag_filter" version="0.1"> | |
2 <description>Use Samtools' view tool to filter alignments based on the flag field.</description> | |
3 <macros> | |
4 <import>samtools_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements"></expand> | |
7 <expand macro="stdio"></expand> | |
8 <expand macro="version_command"></expand> | |
9 | |
10 <command> | |
11 <![CDATA[ | |
12 samtools sort -@ \${GALAXY_SLOTS:-1} -o temp_bam -O bam -T dataset "${input}" && | |
13 samtools view -@ \${GALAXY_SLOTS:-1} | |
14 #for $bit in $bits | |
15 -${bit.state} ${bit.flag} | |
16 #end for | |
17 -b -o "${output}" temp_bam | |
18 ]]> | |
19 </command> | |
20 <inputs> | |
21 <param name="input" format="bam,sam" label="BAM/SAM dataset to filter by flag" type="data" /> | |
22 <repeat name="bits" title="Flag"> | |
23 <param name="flag" type="select" label="Type"> | |
24 <option value="0x0001">Read is paired 0x0001</option> | |
25 <option value="0x0002">Read is mapped in a proper pair 0x0002</option> | |
26 <option value="0x0004">The read is unmapped 0x0004</option> | |
27 <option value="0x0008">The mate is unmapped 0x0008</option> | |
28 <option value="0x0010">Read strand 0x0010</option> | |
29 <option value="0x0020">Mate strand 0x0020</option> | |
30 <option value="0x0040">Read is the first in a pair 0x0040</option> | |
31 <option value="0x0080">Read is the second in a pair 0x0080</option> | |
32 <option value="0x0100">The alignment or this read is not primary 0x0100</option> | |
33 <option value="0x0200">The read fails platform/vendor quality checks 0x0200</option> | |
34 <option value="0x0400">The read is a PCR or optical duplicate 0x0400</option> | |
35 </param> | |
36 <param name="state" type="select" display="radio" label="Set the states for this flag"> | |
37 <option value="f">Keep only alignments with this flag set --f</option> | |
38 <option value="F">Remove all alignments with this flag set --F</option> | |
39 </param> | |
40 </repeat> | |
41 | |
42 </inputs> | |
43 <outputs> | |
44 <data format="bam" name="output" label="Filtered by flag from ${on_string}" /> | |
45 </outputs> | |
46 <tests> | |
47 <test> | |
48 <param ftype="bam" name="input" value="unfiltered.bam" /> | |
49 <param name="bits_0|flag" value="The read is unmapped 0x0004"/> | |
50 <param name="bits_0|state" value="f"/> | |
51 <output file="f0X0004.bam" ftype="bam" name="output" /> | |
52 </test> | |
53 <test> | |
54 <param ftype="bam" name="input" value="unfiltered.bam" /> | |
55 <param name="bits_0|flag" value="The read is unmapped 0x0004"/> | |
56 <param name="bits_0|state" value="f"/> | |
57 <param name="bits_1|flag" value="The mate is unmapped 0x0008"/> | |
58 <param name="bits_1|state" value="f"/> | |
59 <output file="f0X0004_plus8.bam" ftype="bam" name="output" /> | |
60 </test> | |
61 <test> | |
62 <param ftype="bam" name="input" value="unfiltered.bam" /> | |
63 <param name="bits_0|flag" value="The read is unmapped 0x0004"/> | |
64 <param name="bits_0|state" value="f"/> | |
65 <param name="bits_1|flag" value="The mate is unmapped 0x0008"/> | |
66 <param name="bits_1|state" value="F"/> | |
67 <output file="f0X0004_less8.bam" ftype="bam" name="output" /> | |
68 </test> | |
69 </tests> | |
70 <help> | |
71 <![CDATA[ | |
72 This tool uses Samtools view method and specifically the -f and -F parameters to filter a sam file to remove alignments based on their flag field. | |
73 | |
74 Alignments can be excluded based on either the presence or absence of that bit in their flag file. | |
75 | |
76 Multiple check can be carried out in the same pass. | |
77 | |
78 The flag values used are: | |
79 | |
80 0x0001: Read is paired | |
81 | |
82 0x0002: Read is mapped in a proper pair | |
83 | |
84 0x0004: The read is unmapped | |
85 | |
86 0x0008: The mate is unmapped | |
87 | |
88 0x0010: Read strand | |
89 | |
90 0x0020: Mate strand | |
91 | |
92 0x0040: Read is the first in a pair | |
93 | |
94 0x0080: Read is the second in a pair | |
95 | |
96 0x0100: The alignment or this read is not primary | |
97 | |
98 0x0200: The read fails platform/vendor quality checks | |
99 | |
100 0x0400: The read is a PCR or optical duplicate | |
101 ]]> | |
102 </help> | |
103 <expand macro="citations"></expand> | |
104 </tool> |