Mercurial > repos > iuc > bbtools_bbmerge

annotate bbmerge.xml @ 6:cab19c0452c4 draft default tip

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 cd59ba2c349865259b92302a1d70e103b8a5e3cb
author iuc
date Tue, 27 Aug 2024 10:15:19 +0000
parents 1af48f9cc27b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
fc029a9b4d07 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@">
fc029a9b4d07 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>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
3 <macros>
fc029a9b4d07 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>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
5 </macros>
fc029a9b4d07 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"/>
5
1af48f9cc27b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit e6a741fc2fe38e91a310e9c29467c814a2d34cac
iuc
parents: 4
diff changeset
7 <expand macro="bio.tools"/>
0
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
8 <expand macro="requirements"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
9 <command detect_errors="exit_code"><![CDATA[
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
10 #if str($input_type_cond.input_type) in ['single', 'pair']:
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
11 #set read1 = $input_type_cond.read1
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
12 ## bbmerge uses the file extension to determine the input format.
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
13 #set ext = '.fastq'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
14 #if $read1.ext.endswith('.gz'):
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
15 #set ext = $ext + '.gz'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
16 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
17 #set read1_file = 'forward' + $ext
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
18 ln -s '${read1}' '${read1_file}' &&
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
19 #if str($input_type_cond.input_type) == 'pair':
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
20 #set read2 = $input_type_cond.read2
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
21 #set read2_file = 'reverse' + $ext
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
22 ln -s '${read2}' '${read2_file}' &&
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
23 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
24 #else:
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
25 #set read1 = $input_type_cond.reads_collection['forward']
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
26 ## bbmap uses the file extension to determine the input format.
4
5d8b93c0731f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
iuc
parents: 3
diff changeset
27 #set ext = '.fastq'
0
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
28 #if $read1.ext.endswith('.gz'):
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
29 #set ext = $ext + '.gz'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
30 #end if
4
5d8b93c0731f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
iuc
parents: 3
diff changeset
31 #set read1_file = 'forward' + $ext
0
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
32 ln -s '${read1}' '${read1_file}' &&
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
33 #set read2 = $input_type_cond.reads_collection['reverse']
4
5d8b93c0731f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 8f659e3524ff3fbf70ce9f4090e3fe8a49048b29
iuc
parents: 3
diff changeset
34 #set read2_file = 'reverse' + $ext
0
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
35 ln -s '${read2}' '${read2_file}' &&
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
36 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
37
3
82ced0e47b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1cd738ce63dc53cebf13439456e761ef63dc019c
iuc
parents: 0
diff changeset
38 if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then
82ced0e47b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1cd738ce63dc53cebf13439456e761ef63dc019c
iuc
parents: 0
diff changeset
39 export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m";
82ced0e47b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1cd738ce63dc53cebf13439456e761ef63dc019c
iuc
parents: 0
diff changeset
40 fi &&
82ced0e47b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1cd738ce63dc53cebf13439456e761ef63dc019c
iuc
parents: 0
diff changeset
41
82ced0e47b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1cd738ce63dc53cebf13439456e761ef63dc019c
iuc
parents: 0
diff changeset
42 bbmerge.sh tmpdir="\$TMPDIR" t="\${GALAXY_SLOTS:-2}"
82ced0e47b9d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 1cd738ce63dc53cebf13439456e761ef63dc019c
iuc
parents: 0
diff changeset
43
0
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
44 #### Input parameters
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
45 #if str($input_type_cond.input_type) == 'single':
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
46 in='${read1_file}'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
47 interleaved=t
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
48 #else:
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
49 in1='${read1_file}' in2='${read2_file}'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
50 interleaved=f
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
51 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
52
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
53 #### Output options
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
54 out=merged.fastq
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
55 outu=unmerged.fastq
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
56 ihist=ihist.tabular
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
57 touppercase=t
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
58
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
59 #### Quality and trimming parameters
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
60 qtrim='$qt_options.qtrim'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
61 trimq='$qt_options.trimq'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
62 minlength='$qt_options.minlength_after_trim'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
63 usequality='$qt_options.usequality'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
64
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
65 #### Merging parameters
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
66 usejni=f ## Do overlapping in C code, which is faster.
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
67 ecco='$merge_options.ecco'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
68 trimnonoverlapping='$merge_options.trimnonoverlapping'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
69 mininsert='$merge_options.mininsert'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
70 minoverlap='$merge_options.minoverlap'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
71 minq='$merge_options.minq'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
72 maxq='$merge_options.maxq'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
73 entropy='$merge_options.entropy'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
74 efilter='$merge_options.efilter'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
75 pfilter='$merge_options.pfilter'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
76 kfilter='$merge_options.kfilter'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
77 usequality='$merge_options.usequality'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
78
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
79 #if $merge_options.adapters.selector == "with_adaptors":
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
80 adapter1='$merge_options.adapter1'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
81 adapter2='$merge_options.adapter2'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
82 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
83
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
84 #if $merge_options.merge_mode.selector == 'Ratio mode':
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
85 maxratio='$merge_options.merge_mode.maxratio'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
86 ratiomargin='$merge_options.merge_mode.ratiomargin'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
87 ratiooffset='$merge_options.merge_mode.ratiooffset'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
88 maxmismatches='$merge_options.merge_mode.maxmismatches'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
89 ratiominoverlapreduction=0
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
90 minsecondratio='$merge_options.merge_mode.minsecondratio'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
91 #else:
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
92 margin='$merge_options.merge_mode.margin'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
93 mismatches='$merge_options.merge_mode.mismatches'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
94 requireratiomatch='$merge_options.merge_mode.requireratiomatch'
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
95 #end if
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
96
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
97 $merge_options.strictness=t
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
98 ]]></command>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
99 <inputs>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
100 <expand macro="input_type_cond"/>
fc029a9b4d07 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">
fc029a9b4d07 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">
fc029a9b4d07 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>
fc029a9b4d07 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>
fc029a9b4d07 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>
fc029a9b4d07 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>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
107 </param>
fc029a9b4d07 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"/>
fc029a9b4d07 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"/>
fc029a9b4d07 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?"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
111 </section>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
112 <section name="merge_options" title="Merging parameters">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
113 <param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
114 <option value="xstrict">max strict</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
115 <option value="ustrict">ultra strict</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
116 <option value="vstrict">very strict</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
117 <option value="strict">strict</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
118 <option value="default" selected="true">default</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
119 <option value="loose">loose</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
120 <option value="vloose">very loose</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
121 <option value="uloose">ultra loose</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
122 <option value="xloose">max loose</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
123 <option value="fast">fastest possible, less accurate</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
124 </param>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
125 <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."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
126 <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."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
127 <param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
128 <param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
129 <param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
130 <param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
131 <param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
132 <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."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
133 <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."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
134 <param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
135 <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."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
136 <conditional name="adapters">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
137 <param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
138 <option value="wout_adapters" selected="true">No</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
139 <option value="with_adapters">Yes, use these adapter sequences</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
140 </param>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
141 <when value="wout_adapters"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
142 <when value="with_adapters">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
143 <param argument="adapter1" type="text" value="" label="Left adapter sequence"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
144 <param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
145 </when>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
146 </conditional>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
147 <conditional name="merge_mode">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
148 <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.">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
149 <option value="Ratio mode" selected="true">Ratio mode</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
150 <option value="Flat mode">Flat mode</option>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
151 </param>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
152 <when value="Ratio mode">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
153 <param argument="maxratio" type="float" value="0.09" label="Max error rate; higher increases merge rate."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
154 <param argument="ratiomargin" type="float" value="5.5" label="Lower increases merge rate; min is 1."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
155 <param argument="ratiooffset" type="float" value="0.55" label="Lower increases merge rate; min is 0."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
156 <param argument="maxmismatches" type="integer" value="20" label="Maximum mismatches allowed in overlapping region."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
157 <param argument="minsecondratio" type="float" value="0.1" label="Cutoff for second-best overlap ratio."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
158 </when>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
159 <when value="Flat mode">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
160 <param argument="margin" type="integer" value="2" label="The best overlap must have at least 'margin' fewer mismatches than the second best."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
161 <param argument="mismatches" type="integer" value="3" label="Do not allow more than this many mismatches."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
162 <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."/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
163 </when>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
164 </conditional>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
165 </section>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
166 </inputs>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
167 <outputs>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
168 <data format="fastq" name="output_merged_reads" from_work_dir="merged.fastq" label="${tool.name} on ${on_string} (merged reads)"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
169 <data format="fastq" name="output_unmerged_reads" from_work_dir="unmerged.fastq" label="${tool.name} on ${on_string} (unmerged reads)"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
170 <data format="tabular" name="output_insertlen_hist" from_work_dir="ihist.tabular" label="${tool.name} on ${on_string} (insert size histogram)"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
171 </outputs>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
172 <tests>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
173 <!-- Single interleaved file -->
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
174 <test expect_num_outputs="3">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
175 <param name="input_type" value="single"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
176 <param name="read1" value="bbmerge/input_interleaved.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
177 <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
178 <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
179 <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
180 </test>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
181 <!-- Paired mates in 2 separate files -->
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
182 <test expect_num_outputs="3">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
183 <param name="input_type" value="pair"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
184 <param name="read1" value="bbmerge/input_R1.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
185 <param name="read2" value="bbmerge/input_R2.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
186 <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
187 <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
188 <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
189 </test>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
190 <!-- Paired mates provided via a paired collection -->
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
191 <test expect_num_outputs="3">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
192 <param name="input_type" value="paired"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
193 <param name="reads_collection">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
194 <collection type="paired">
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
195 <element name="forward" value="bbmerge/input_R1.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
196 <element name="reverse" value="bbmerge/input_R2.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
197 </collection>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
198 </param>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
199 <output name="output_unmerged_reads" ftype="fastq" value="bbmerge/unmerged.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
200 <output name="output_merged_reads" ftype="fastq" value="bbmerge/merged.fastq"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
201 <output name="output_insertlen_hist" ftype="tabular" value="bbmerge/insert_length_hist.tabular"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
202 </test>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
203 </tests>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
204 <help>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
205 **What it does**
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
206
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
207 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.
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
208
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
209 -----
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
210
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
211 **A Martian PE sequencing result is expected to be processed as follows:**
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
212
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
213 input_R1.fastq::
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
214
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
215 @read_header_1/1
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
216 AAAAATTTTTAAAAACCCCCGGGGG
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
217 +
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
218 FFFFFFFFFFFFFFFEFFFFFF,FF
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
219 @read_header_2/1
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
220 AAAATTTTAAAACCCCCGGGGG
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
221 +
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
222 FFFFFFFFFFFFFFFEFFFFFF
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
223
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
224
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
225 input_R2.fastq::
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
226
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
227 @read_header_1/2
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
228 TTAATTAATTCCCCCGGGGG
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
229 +
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
230 FFFFFFFFFFFFFFFFFFFF
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
231 @read_header_2/2
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
232 TTTAAATTTAAACCCCCGGGGG
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
233 +
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
234 FFFFFFFFFFFFFFFFFFFFEF
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
235
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
236
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
237 output.fastq::
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
238
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
239 @read_header_1
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
240 AAAAATTTTTAAAAACCCCCGGGGGAATTAATTAA
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
241 +
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
242 FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
243 @read_header_2
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
244 AAAATTTTAAAACCCCCGGGGGTTTAAATTTAAA
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
245 +
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
246 FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
247 </help>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
248 <expand macro="citations"/>
fc029a9b4d07 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit aca07f4e7d683d1b7d06abb63e05d4ff1b28771f
iuc
parents:
diff changeset
249 </tool>