Mercurial > repos > iuc > ngsutils_bam_filter

annotate bam_filter.xml @ 0:4e4e4093d65d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
author iuc
date Wed, 11 Nov 2015 13:04:07 -0500
parents
children 8187a729d9f4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
1 <tool id="ngsutils_bam_filter" name="BAM filter" version="@WRAPPER_VERSION@.0">
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
2 <description>Removes reads from a BAM file based on criteria</description>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
3 <macros>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
4 <import>macros.xml</import>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
5 </macros>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
6 <expand macro="requirements" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
7 <expand macro="stdio" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
8 <expand macro="version" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
9 <command><![CDATA[
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
10 ## If the tool is executed with no filtering option,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
11 ## the default parameters simply copy over the input file
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
12 if grep -q "\w" ${parameters};
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
13 then
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
14 $__tool_directory__/filter.py
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
15 $infile
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
16 $outfile
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
17 `cat ${parameters}`;
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
18 else
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
19 cp $infile $outfile;
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
20 fi
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
21 ]]>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
22 </command>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
23 <configfiles>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
24 <configfile name="parameters">
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
25 <![CDATA[
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
26 #if $minlen:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
27 -minlen $minlen
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
28 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
29 #if $maxlen
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
30 -maxlen $maxlen
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
31 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
32 $mapped
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
33 $unmapped
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
34 $properpair
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
35 $noproperpair
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
36 #if $mask:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
37 -mask "${mask}"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
38 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
39 #if int($uniq) > -1:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
40 -uniq
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
41 #if int($uniq) > 0:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
42 $uniq
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
43 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
44 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
45 $uniq_start
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
46 #if $mismatch:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
47 -mismatch $mismatch
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
48 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
49 $nosecondary
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
50 $noqcfail
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
51 $nopcrdup
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
52 #if $excludebed:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
53 -excludebed "${excludebed}" $ignore_strand
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
54 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
55 #if $includebed:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
56 -includebed "${includebed}" $ignore_strand
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
57 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
58 #if $includeref:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
59 -includeref "${includeref}"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
60 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
61 #if $excluderef:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
62 -excluderef "${excluderef}"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
63 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
64 #if $maximum_mismatch_ratio
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
65 -maximum_mismatch_ratio $maximum_mismatch_ratio
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
66 #end if
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
67 ]]>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
68 </configfile>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
69 </configfiles>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
70 <inputs>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
71 <param name="infile" type="data" format="bam" label="Select BAM dataset" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
72 <param argument="-minlen" type="integer" value="" optional="True" min="0"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
73 label="Remove reads that are smaller than"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
74 help="in bp"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
75 <param argument="-maxlen" type="integer" value="" optional="True" min="0"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
76 label="Remove reads that are larger than"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
77 help="in bp"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
78 <param argument="-mapped" truevalue="-mapped" type="boolean" falsevalue=""
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
79 label="Keep only mapped reads"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
80 help="" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
81 <param argument="-unmapped" truevalue="-unmapped" type="boolean" falsevalue=""
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
82 label="Keep only unmapped reads"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
83 help="" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
84 <param argument="-properpair" truevalue="-properpair" type="boolean" falsevalue=""
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
85 label="Keep only properly paired reads"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
86 help="both mapped, correct orientation, flag set in BAM" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
87 <param argument="-noproperpair" truevalue="-noproperpair" type="boolean" falsevalue=""
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
88 label="Discard properly paired reads"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
89 help="" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
90 <param argument="-mask" type="text" value="" optional="True" label="Remove reads that match the mask"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
91 help="e.g. 0x400, 0x2" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
92
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
93 <param argument="-uniq" type="integer" value="-1" optional="True" min="-1"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
94 label="Remove reads that have the same sequence"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
95 help="up to the Nth nucleotide starting from the 5prime end. -1 means do not filter, 0 means check along the entire read,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
96 10 would make filter reads that are unique over the first 10 nucleotides."/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
97
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
98 <param argument="-uniq_start" truevalue="-uniq_start" type="boolean" falsevalue=""
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
99 label="Remove reads that start at the same position"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
100 help="Use only for low-coverage samples" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
101
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
102 <param argument="-mismatch" type="integer" value="" optional="True" min="0"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
103 label="Remove reads with that many mismatches"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
104 help="Indels always counts as 1 regardless of length. Requires NM tag to be set."/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
105
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
106 <param argument="-nosecondary" truevalue="-nosecondary" type="boolean" falsevalue=""
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
107 label="Remove secondary alignment reads"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
108 help="Remove reads flagged with 0x100" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
109 <param argument="-noqcfail" truevalue="-noqcfail" type="boolean" falsevalue=""
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
110 label="Remove reads that do not pass the quality control"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
111 help="Remove reads flagged with 0x200" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
112 <param argument="-nopcrdup" truevalue="-nopcrdup" type="boolean" falsevalue=""
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
113 label="Remove reads that are marked as PCR dupicates "
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
114 help="Remove reads flagged with 0x400" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
115
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
116 <param argument="-excludebed" type="data" optional="True" format="bed" label="Remove reads that are in any of the regions" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
117 <param argument="-includebed" type="data" optional="True" format="bed" label="Remove reads that are NOT any of the regions" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
118 <param name="ignore_strand" truevalue="nostrand" type="boolean" falsevalue=""
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
119 label="Strand information from BED file is ignored. Affects -excludebed and -includebed."
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
120 help="" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
121
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
122 <param argument="-includeref" type="text" value="" optional="True" label="Exclude reads NOT mapped to a reference"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
123 help="" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
124 <param argument="-excluderef" type="text" value="" optional="True" label="Exclude reads mapped to a particular reference"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
125 help="e.g. chrM, or _dup chromosomes" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
126
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
127 <param argument="-maximum_mismatch_ratio" type="float" value="" optional="True" min="0.0" max="1.0"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
128 label="Filter by maximum mismatch ratio"
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
129 help="fraction of length"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
130
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
131 </inputs>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
132 <outputs>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
133 <data format="bam" name="outfile" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
134 </outputs>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
135 <tests>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
136 <test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
137 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
138 <param name="minlen" value="100"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
139 <param name="maximum_mismatch_ratio" value="0.02"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
140 <output name="outfile" file="ngsutils_bam_filter_result1.bam" ftype="bam" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
141 </test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
142 <test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
143 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
144 <param name="minlen" value="250"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
145 <param name="properpair" value="True"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
146 <output name="outfile" file="ngsutils_bam_filter_result2.bam" ftype="bam" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
147 </test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
148 <test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
149 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
150 <param name="minlen" value="100"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
151 <param name="nosecondary" value="True"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
152 <param name="noqcfail" value="True"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
153 <param name="nopcrdup" value="True"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
154 <output name="outfile" file="ngsutils_bam_filter_result3.bam" ftype="bam" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
155 </test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
156 <test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
157 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
158 <output name="outfile" file="ngsutils_bam_filter_input1.bam" ftype="bam" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
159 </test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
160 <test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
161 <param name="infile" ftype="bam" value="ngsutils_bam_filter_input1.bam"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
162 <param name="mask" value="0x40"/>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
163 <output name="outfile" file="ngsutils_bam_filter_result4.bam" ftype="bam" />
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
164 </test>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
165 </tests>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
166 <help><![CDATA[
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
167 Removes reads from a BAM file based on criteria.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
168
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
169 Given a BAM file, this tool will discard reads that did not meet the selected filtering criteria
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
170 The output is another BAM file with the reads not matching the criteria removed.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
171
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
172 Note: this does not adjust tag values reflecting any filtering. (for example:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
173 if a read mapped to two locations (IH:i:2), and one was removed by
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
174 filtering, the IH:i tag would still read IH:i:2).
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
175
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
176 Currently, the available filters are:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
177
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
178 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
179 | Agument | Description |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
180 +================================+=================================================+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
181 | -minlen val | Remove reads that are smaller than {val} |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
182 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
183 | -maxlen val | Remove reads that are larger than {val} |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
184 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
185 | -mapped | Keep only mapped reads |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
186 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
187 | -unmapped | Keep only unmapped reads |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
188 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
189 | -properpair | Keep only properly paired reads (both mapped, |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
190 | | correct orientation, flag set in BAM) |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
191 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
192 | -noproperpair | Keep only not-properly paired reads |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
193 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
194 | -mask bitmask | Remove reads that match the mask (e.g. 0x400) |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
195 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
196 | -uniq {length} | Remove reads that are have the same sequence |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
197 | | Note: BAM file should be sorted |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
198 | | (up to an optional length) |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
199 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
200 | -uniq_start | Remove reads that start at the same position |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
201 | | Note: BAM file should be sorted |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
202 | | (Use only for low-coverage samples) |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
203 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
204 |-mismatch num | Number of mismatches or indels |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
205 | | indel always counts as 1 regardless of length |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
206 | | (requires NM tag in reads) |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
207 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
208 |-nosecondary | Remove reads that have the 0x100 flag set |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
209 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
210 |-noqcfail | Remove reads that have the 0x200 flag set |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
211 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
212 |-nopcrdup | Remove reads that have the 0x400 flag set |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
213 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
214 |-excludebed file.bed {nostrand} | Remove reads that are in any of the regions |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
215 | | from the given BED file. If 'nostrand' is given,|
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
216 | | strand information from the BED file is ignored.|
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
217 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
218 |-includebed file.bed {nostrand} | Remove reads that are NOT any of the regions |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
219 | | from the given BED file. If 'nostrand' is given,|
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
220 | | strand information from the BED file is ignored.|
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
221 | | Note: If this is a large dataset, use |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
222 | | "bamutils extract" instead. |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
223 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
224 | -includeref refname | Exclude reads NOT mapped to a reference |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
225 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
226 | -excluderef refname | Exclude reads mapped to a particular reference |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
227 | | (e.g. chrM, or _dup chromosomes) |
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
228 +--------------------------------+-------------------------------------------------+
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
229 ]]>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
230 </help>
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
231 </tool>