Mercurial > repos > iuc > bbtools_bbmerge

annotate bbmerge.xml @ 0:a669d974b9bc 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/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
author iuc
date Mon, 06 Feb 2023 18:05:24 +0000
parents
children 16db2a5b73c5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
1 <tool id="bbtools_bbmerge" name="BBTools: BBMerge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
2 <description>Merge overlapping mates of a read pair</description>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
3 <macros>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
4 <import>macros.xml</import>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
5 </macros>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
6 <expand macro="edam_ontology"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
7 <expand macro="requirements"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
9 #import os
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
10 #import re
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
11
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
12 #if str($input_type_cond.input_type) in ['single', 'pair']:
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
13 #set read1 = $input_type_cond.read1
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
14 ## bbmerge uses the file extension to determine the input format.
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
15 #set ext = '.fastq'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
16 #if $read1.ext.endswith('.gz'):
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
17 #set ext = $ext + '.gz'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
18 #end if
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
19 #set read1_file = 'forward' + $ext
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
20 ln -s '${read1}' '${read1_file}' &&
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
21 #if str($input_type_cond.input_type) == 'pair':
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
22 #set read2 = $input_type_cond.read2
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
23 #set read2_file = 'reverse' + $ext
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
24 ln -s '${read2}' '${read2_file}' &&
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
25 #end if
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
26 #else:
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
27 #set read1 = $input_type_cond.reads_collection['forward']
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
28 #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
29 ## bbmap uses the file extension to determine the input format.
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
30 #set ext = $read1_identifier + '.fastq'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
31 #if $read1.ext.endswith('.gz'):
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
32 #set ext = $ext + '.gz'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
33 #end if
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
34 #set read1_file = $read1_identifier + $ext
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
35 ln -s '${read1}' '${read1_file}' &&
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
36 #set read2 = $input_type_cond.reads_collection['reverse']
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
37 #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
38 #set read2_file = $read2_identifier + $ext
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
39 ln -s '${read2}' '${read2_file}' &&
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
40 #end if
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
41
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
42 bbmerge.sh
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
43 #### Input parameters
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
44 #if str($input_type_cond.input_type) == 'single':
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
45 in='${read1_file}'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
46 interleaved=t
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
47 #else:
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
48 in1='${read1_file}' in2='${read2_file}'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
49 interleaved=f
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
50 #end if
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
51
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
52 #### Output options
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
53 out=merged.fastq
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
54 outu=unmerged.fastq
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
55 ihist=ihist.tabular
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
56 touppercase=t
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
57
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
58 #### Quality and trimming parameters
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
59 qtrim='$qt_options.qtrim'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
60 trimq='$qt_options.trimq'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
61 minlength='$qt_options.minlength_after_trim'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
62 usequality='$qt_options.usequality'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
63
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
64 #### Merging parameters
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
65 usejni=f ## Do overlapping in C code, which is faster.
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
66 ecco='$merge_options.ecco'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
67 trimnonoverlapping='$merge_options.trimnonoverlapping'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
68 mininsert='$merge_options.mininsert'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
69 minoverlap='$merge_options.minoverlap'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
70 minq='$merge_options.minq'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
71 maxq='$merge_options.maxq'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
72 entropy='$merge_options.entropy'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
73 efilter='$merge_options.efilter'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
74 pfilter='$merge_options.pfilter'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
75 kfilter='$merge_options.kfilter'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
76 usequality='$merge_options.usequality'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
77
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
78 #if $merge_options.adapters.selector == "with_adaptors":
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
79 adapter1='$merge_options.adapter1'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
80 adapter2='$merge_options.adapter2'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
81 #end if
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
82
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
83 #if $merge_options.merge_mode.selector == 'Ratio mode':
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
84 maxratio='$merge_options.merge_mode.maxratio'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
85 ratiomargin='$merge_options.merge_mode.ratiomargin'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
86 ratiooffset='$merge_options.merge_mode.ratiooffset'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
87 maxmismatches='$merge_options.merge_mode.maxmismatches'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
88 ratiominoverlapreduction=0
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
89 minsecondratio='$merge_options.merge_mode.minsecondratio'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
90 #else:
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
91 margin='$merge_options.merge_mode.margin'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
92 mismatches='$merge_options.merge_mode.mismatches'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
93 requireratiomatch='$merge_options.merge_mode.requireratiomatch'
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
94 #end if
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
95
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
96 $merge_options.strictness=t
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
97 ]]></command>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
98 <inputs>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
99 <expand macro="input_type_cond"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
100
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
101 <section name="qt_options" title="Quality and trimming options">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
102 <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
103 <option value="f" selected="true">No trimming</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
104 <option value="l">Trim left</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
105 <option value="r">Trim right</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
106 <option value="lr">Trim both</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
107 </param>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
108 <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
109 <param argument="minlength_after_trim" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
110 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
111 </section>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
112
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
113 <section name="merge_options" title="Merging parameters">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
114 <param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
115 <option value="xstrict">max strict</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
116 <option value="ustrict">ultra strict</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
117 <option value="vstrict">very strict</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
118 <option value="strict">strict</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
119 <option value="default" selected="true">default</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
120 <option value="loose">loose</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
121 <option value="vloose">very loose</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
122 <option value="uloose">ultra loose</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
123 <option value="xloose">max loose</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
124 <option value="fast">fastest possible, less accurate</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
125 </param>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
126 <param argument="ecco" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Error-correct the overlapping part, but don't merge." help="If selected, the tool with find the overlaps as if merging reads, use this overlap information to correct sequencing errors on both strands. However, the strands from the mates will not be merged but provided as two separate reads after error correction."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
127 <param argument="trimnonoverlapping" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim all non-overlapping portions, leaving only consensus sequence. By default, only sequence to the right of the overlap (adapter sequence) is trimmed."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
128 <param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
129 <param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
130
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
131 <param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
132 <param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
133
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
134 <param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
135 <param argument="efilter" type="integer" value="6" label="Ban overlaps with over this many times the expected number of errors." help="Lower is more strict, -1 disables."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
136 <param argument="pfilter" type="float" value="0.00004" label="Probability filter to disallow improbable overlaps." help="Higher is stricter. 0 will disable the filter; 1 will allow only perfect overlaps."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
137 <param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
138 <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Take quality factors into account" help="If disabled, quality values are completely ignored, both for overlap detection and filtering. May be useful for data with inaccurate quality values."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
139
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
140 <conditional name="adapters">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
141 <param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
142 <option value="wout_adapters" selected="true">No</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
143 <option value="with_adapters">Yes, use these adapter sequences</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
144 </param>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
145 <when value="wout_adapters"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
146 <when value="with_adapters">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
147 <param argument="adapter1" type="text" value="" label="Left adapter sequence"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
148 <param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
149 </when>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
150 </conditional>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
151
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
152 <conditional name="merge_mode">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
153 <param name="selector" type="select" label="Evaluate overlaps via..." help="In the ratio mode, overlaps are decided based on the ratio of matching to mismatching bases. Flat mode scores overlaps based on the total number of mismatching bases only.">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
154 <option value="Ratio mode" selected="true">Ratio mode</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
155 <option value="Flat mode">Flat mode</option>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
156 </param>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
157 <when value="Ratio mode">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
158 <param argument="maxratio" type="float" value="0.09" label="Max error rate; higher increases merge rate."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
159 <param argument="ratiomargin" type="float" value="5.5" label="Lower increases merge rate; min is 1."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
160 <param argument="ratiooffset" type="float" value="0.55" label="Lower increases merge rate; min is 0."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
161 <param argument="maxmismatches" type="integer" value="20" label="Maximum mismatches allowed in overlapping region."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
162 <param argument="minsecondratio" type="float" value="0.1" label="Cutoff for second-best overlap ratio."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
163 </when>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
164 <when value="Flat mode">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
165 <param argument="margin" type="integer" value="2" label="The best overlap must have at least 'margin' fewer mismatches than the second best."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
166 <param argument="mismatches" type="integer" value="3" label="Do not allow more than this many mismatches."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
167 <param argument="requireratiomatch" type="boolean" value="false" label="Require the answer from flat mode and ratio mode to agree, reducing false positives if both are enabled."/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
168 </when>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
169 </conditional>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
170 </section>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
171 </inputs>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
172 <outputs>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
173 <data format="fastq" name="output_merged_reads" from_work_dir="merged.fastq" label="${tool.name} on ${on_string} (merged reads)"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
174 <data format="fastq" name="output_unmerged_reads" from_work_dir="unmerged.fastq" label="${tool.name} on ${on_string} (unmerged reads)"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
175 <data format="tabular" name="output_insertlen_hist" from_work_dir="ihist.tabular" label="${tool.name} on ${on_string} (insert size histogram)"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
176 </outputs>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
177 <tests>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
178 <!-- Single interleaved file -->
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
179 <test expect_num_outputs="3">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
180 <param name="input_type" value="single"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
181 <param name="read1" value="bbmerge/input_interleaved.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
182 <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
183 <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
184 <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
185 </test>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
186 <!-- Paired mates in 2 separate files -->
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
187 <test expect_num_outputs="3">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
188 <param name="input_type" value="pair"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
189 <param name="read1" value="bbmerge/input_R1.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
190 <param name="read2" value="bbmerge/input_R2.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
191 <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
192 <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
193 <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
194 </test>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
195 <!-- Paired mates provided via a paired collection -->
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
196 <test expect_num_outputs="3">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
197 <param name="input_type" value="paired"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
198 <param name="reads_collection">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
199 <collection type="paired">
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
200 <element name="forward" value="bbmerge/input_R1.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
201 <element name="reverse" value="bbmerge/input_R2.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
202 </collection>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
203 </param>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
204 <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
205 <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
206 <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
207 </test>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
208 </tests>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
209 <help>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
210 **What it does**
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
211
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
212 BBMerge merges two overlapping paired reads into a single read. A 2x100nt read pair, for instance can be merged into a single read of length 150nt if the last 50nt of the first read mate and the last 50nt of the second read map overlap. The accuracy of the base calling can also improve as a result of such a reconciliation between the read pairs. BBMerge is also capable of error-correcting the overlapping portion of reads without merging them, as well as merging nonoverlapping reads, if enough coverage is available.
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
213
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
214 -----
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
215
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
216 **A Martian PE sequencing result is expected to be processed as follows:**
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
217
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
218 input_R1.fastq::
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
219
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
220 @read_header_1/1
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
221 AAAAATTTTTAAAAACCCCCGGGGG
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
222 +
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
223 FFFFFFFFFFFFFFFEFFFFFF,FF
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
224 @read_header_2/1
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
225 AAAATTTTAAAACCCCCGGGGG
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
226 +
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
227 FFFFFFFFFFFFFFFEFFFFFF
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
228
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
229
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
230 input_R2.fastq::
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
231
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
232 @read_header_1/2
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
233 TTAATTAATTCCCCCGGGGG
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
234 +
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
235 FFFFFFFFFFFFFFFFFFFF
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
236 @read_header_2/2
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
237 TTTAAATTTAAACCCCCGGGGG
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
238 +
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
239 FFFFFFFFFFFFFFFFFFFFEF
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
240
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
241
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
242 output.fastq::
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
243
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
244 @read_header_1
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
245 AAAAATTTTTAAAAACCCCCGGGGGAATTAATTAA
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
246 +
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
247 FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
248 @read_header_2
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
249 AAAATTTTAAAACCCCCGGGGGTTTAAATTTAAA
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
250 +
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
251 FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
252 </help>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
253 <expand macro="citations"/>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
254 </tool>
a669d974b9bc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
255