/tools/indels/indel_sam2interval.xml
XML | 139 lines | 133 code | 6 blank | 0 comment | 0 complexity | 724de95e9dfbf156255c14e272e66eac MD5 | raw file
1<tool id="indel_sam2interval" name="Extract indels" version="1.0.0"> 2 <description>from SAM</description> 3 <command interpreter="python"> 4 indel_sam2interval.py 5 --input=$input1 6 --include_base=$include_base 7 --collapse=$collapse 8 --int_out=$output1 9 #if $ins_out.include_ins_out == "true" 10 --bed_ins_out=$output2 11 #else 12 --bed_ins_out="None" 13 #end if 14 #if $del_out.include_del_out == "true" 15 --bed_del_out=$output3 16 #else 17 --bed_del_out="None" 18 #end if 19 </command> 20 <inputs> 21 <param format="sam" name="input1" type="data" label="Select dataset to convert" /> 22 <param name="include_base" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Include the relevant base(s) for each insertion (and a dash (-) for deletions)" /> 23 <param name="collapse" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Collapse repeated locations onto single line with counts" /> 24 <conditional name="ins_out"> 25 <param name="include_ins_out" type="select" label="Include insertions output bed file?"> 26 <option value="true">Yes</option> 27 <option value="false">No</option> 28 </param> 29 <when value="true" /> 30 <when value="false" /> 31 </conditional> 32 <conditional name="del_out"> 33 <param name="include_del_out" type="select" label="Include deletions output bed file?"> 34 <option value="true">Yes</option> 35 <option value="false">No</option> 36 </param> 37 <when value="true" /> 38 <when value="false" /> 39 </conditional> 40 </inputs> 41 <outputs> 42 <data format="interval" name="output1" /> 43 <data format="bed" name="output2"> 44 <filter>ins_out[ "include_ins_out" ] == "true"</filter> 45 </data> 46 <data format="bed" name="output3"> 47 <filter>del_out[ "include_del_out" ] == "true"</filter> 48 </data> 49 </outputs> 50 <tests> 51 <test> 52 <param name="input1" value="indel_sam2interval_in1.sam" ftype="sam"/> 53 <param name="include_base" value="true"/> 54 <param name="collapse" value="true"/> 55 <param name="include_ins_out" value="true" /> 56 <param name="include_del_out" value="true" /> 57 <output name="output1" file="indel_sam2interval_out1.interval" ftype="interval"/> 58 <output name="output2" file="indel_sam2interval_out2.bed" ftype="bed"/> 59 <output name="output3" file="indel_sam2interval_out3.bed" ftype="bed"/> 60 </test> 61 </tests> 62 <help> 63 64**What it does** 65 66Given a SAM file containing indels, converts these to an interval file with a column indicating whether it is an insertion or a deletion, and then also can create a BED file for each type (one for insertions, one for deletions). The interval file can be combined with other like files to create a table useful for analysis with the Indel Analysis Table tool. The BED files can be useful for visualizing the reads. 67 68----- 69 70**Example** 71 72Suppose you have the following mapping results:: 73 74 r327 16 chrM 11 37 8M1D10M * 0 0 CTTACCAGATAGTCATCA -+<2;?@BA@?-,.+4=4 XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:41^C35 75 r457 0 chr1 14 37 14M * 0 0 ACCTGACAGATATC =/DF;?@1A@?-,. XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 76 r501 16 chrM 6 23 7M1I13M * 0 0 TCTGTGCCTACCAGACATTCA +=$2;?@BA@?-,.+4=4=4A XT:A:U NM:i:3 X0:i:1 X1:i:1 XM:i:2 XO:i:1 XG:i:1 MD:Z:28C36G9 XA:Z:chrM,+134263658,14M1I61M,4; 77 r1288 16 chrM 8 37 11M1I7M * 0 0 TCACTTACCTGTACACACA /*F2;?@%A@?-,.+4=4= XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T0T1A69 78 r1902 0 chr1 4 37 7M2D18M * 0 0 AGTCTCTTACCTGACGGTTATGA <2;?@BA@?-,.+4=4=4AA663 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0 79 r2204 16 chrM 9 0 19M * 0 0 CTGGTACCTGACAGGTATC 2;?@BA@?-,.+4=4=4AA XT:A:R NM:i:1 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T75 XA:Z:chrM,-564927,76M,1; 80 r2314 16 chrM 6 37 10M2D8M * 0 0 TCACTCTTACGTCTGA <2;?@BA@?-,.+4=4 XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:25A5^CA45 81 r3001 0 chrM 13 37 3M1D5M2I7M * 0 0 TACAGTCACCCTCATCA <2;?@BA/(@?-,$& XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0 82 r3218 0 chr1 13 37 8M1D7M * 0 0 TACAGTCACTCATCA <2;?@BA/(@?-,$& XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:2 MD:Z:17^CA58A0 83 r4767 16 chr2 3 37 15M2I7M * 0 0 CAGACTCTCTTACCAAAGACAGAC <2;?@BA/(@?-,.+4=4=4AA66 XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:2T1A4T65 84 r5333 0 chrM 5 37 17M1D8M * 0 0 GTCTCTCATACCAGACAACGGCAT FB3$@BA/(@?-,.+4=4=4AA66 XT:A:U NM:i:4 X0:i:1 X1:i:0 XM:i:3 XO:i:1 XG:i:1 MD:Z:45C10^C0C5C13 85 r6690 16 chrM 7 23 20M * 0 0 CTCTCTTACCAGACAGACAT 2;?@BA/(@?-,.+4=4=4A XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 XA:Z:chrM,-568532,76M,1; 86 r7211 0 chrM 7 37 24M * 0 0 CGACAGAGACAAAATAACATTTAA //<2;?@BA@?-,.+4=442;;6: XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:2 XO:i:1 XG:i:1 MD:Z:73G0G0 87 r7899 69 * 0 0 * * 0 0 CTGCGTGTTGGTGTCTACTGGGGT #%#'##$#$##&%#%$$$%#%#'# 88 r9192 133 * 0 0 * * 0 0 GTGCGTCGGGGAGGGTGCTGTCGG ######%#$%#$$###($###&&% 89 r9922 16 chrM 4 0 7M3I9M * 0 0 CCAGACATTTGAAATCAGG F/D4=44^D++26632;;6 XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 90 r9987 16 chrM 4 0 9M1I18M * 0 0 AGGTTCTCATTACCTGACACTCATCTTG G/AD6"/+4=4426632;;6:<2;?@BA XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 91 r10145 16 chr1 16 0 5M2D7M * 0 0 CACATTGTTGTA G//+4=44=4AA XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 92 r10324 16 chrM 15 0 6M1D5M * 0 0 CCGTTCTACTTG A@??8.G//+4= XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 93 r12331 16 chrM 17 0 4M2I6M * 0 0 AGTCGAATACGTG 632;;6:<2;?@B XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 94 r12914 16 chr2 24 0 4M3I3M * 0 0 ACTACCCCAA G//+4=42,. XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 95 r13452 16 chrM 13 0 3M1D11M * 0 0 TACGTCACTCATCA IIIABCCCICCCCI XT:A:U NM:i:0 X0:i:1 X1:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 96 97 98The following three files will be produced (Interval, Insertions BED and Deletions BED):: 99 100 chr1 11 13 D - 1 101 chr1 21 22 D - 1 102 chr1 21 23 D - 1 103 chr2 18 19 I AA 1 104 chr2 28 29 I CCC 1 105 chrM 11 12 I TTT 1 106 chrM 13 14 I C 1 107 chrM 13 14 I T 1 108 chrM 16 17 D - 1 109 chrM 16 18 D - 1 110 chrM 19 20 D - 1 111 chrM 19 20 I T 1 112 chrM 21 22 D - 1 113 chrM 21 22 I GA 1 114 chrM 22 23 D - 1 115 116 chr2 18 19 117 chr2 28 29 118 chrM 11 12 119 chrM 13 14 120 chrM 13 14 121 chrM 19 20 122 chrM 21 22 123 124 chr1 11 13 125 chr1 21 22 126 chr1 21 23 127 chrM 16 17 128 chrM 16 18 129 chrM 19 20 130 chrM 21 22 131 chrM 22 23 132 133For more information on SAM, please consult the `SAM format description`__. 134 135.. __: http://www.ncbi.nlm.nih.gov/pubmed/19505943 136 137 138 </help> 139</tool>