Mercurial > repos > nml > smalt

annotate smalt_map.xml @ 1:fae9ec82e10f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
author nml
date Wed, 17 Jun 2020 09:47:13 -0400
parents 51ad86498414
children 5ba47ab90254
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
1 <tool id="smalt" name="smalt" version="@VERSION@+galaxy0">
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
2 <description>Map query reads (FASTA/FASTQ) format onto the reference sequences</description>
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
3 <macros>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
4 <token name="@VERSION@">0.7.6</token>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
5 <token name="@INPUT_TYPES@">fastq,fastq.gz,fastqsanger,fastqsanger.gz</token>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
6 </macros>
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
7 <requirements>
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
8 <requirement type="package" version="@VERSION@">smalt</requirement>
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
9 <requirement type="package" version="1.5">samtools</requirement>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
10 </requirements>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
11 <stdio>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
12 <exit_code range="1:" level="fatal" description="Unknown error" />
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
13 <regex match="Command line error"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
14 source="stdout"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
15 level="fatal"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
16 description="You cannot do that!! What were you thinking!" />
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
17 <regex match="ERROR"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
18 source="stderr"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
19 level="fatal"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
20 description="You cannot do that!! What were you thinking!" />
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
21 </stdio>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
22 <command>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
23 <![CDATA[
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
24 ## prepare smalt index
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
25 smalt index
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
26
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
27 #if $k:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
28 -k "$k"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
29 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
30
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
31 #if $s:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
32 -s "$s"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
33 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
34
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
35 'temp' "$reference" &&
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
36
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
37 smalt map
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
38
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
39 -o $output
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
40
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
41 #if $oformat.outformat == "sam":
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
42 #if $oformat.samOptions:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
43 -f "$oformat.outformat:$oformat.samOptions"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
44 #else
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
45 -f "$oformat.outformat"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
46 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
47 #elif $oformat.outformat == "bam":
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
48 #if $oformat.bamOptions:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
49 -f "$oformat.outformat:$oformat.bamOptions"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
50 #else
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
51 -f "$oformat.outformat"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
52 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
53 #else
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
54 -f "$oformat.outformat"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
55 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
56
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
57
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
58
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
59 -n \${GALAXY_SLOTS:-2}
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
60
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
61 #if $singlePaired.sPaired != "single":
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
62 -l $singlePaired.pairtype
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
63 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
64
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
65
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
66 #if $mincover:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
67 -c "$mincover"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
68 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
69
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
70 #if $scordiff:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
71 -d "$scordiff"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
72 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
73
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
74 #if $insfil:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
75 -g "$insfil"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
76 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
77
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
78 #if $insertmax:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
79 -i "$insertmax"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
80 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
81
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
82 #if $insertmin:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
83 -j "$insertmin"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
84 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
85
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
86 #if $minscor:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
87 -m "$minscor"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
88 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
89
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
90 #if $minbasq:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
91 -q "$minbasq"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
92 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
93
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
94 #if $seed:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
95 -r "$seed"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
96 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
97
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
98 #if $sw_weighted:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
99 -w
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
100 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
101
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
102 #if $search_harder:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
103 -x
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
104 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
105
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
106 #if $minid:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
107 -y "$minid"
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
108 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
109
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
110
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
111 'temp'
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
112
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
113 #if $singlePaired.sPaired == "single":
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
114 $singlePaired.sInput1
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
115 #elif $singlePaired.sPaired == "paired":
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
116 $singlePaired.pInput1 $singlePaired.pInput2
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
117 #elif $singlePaired.sPaired == "collections":
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
118 $singlePaired.fastq_collection.forward $singlePaired.fastq_collection.reverse
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
119 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
120
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
121
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
122 #if $oformat.outformat == "bam":
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
123 && samtools sort -@ \${GALAXY_SLOTS:-1} $output -o sorted && mv sorted $output
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
124 #end if
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
125
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
126
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
127 ]]>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
128 </command>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
129
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
130
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
131 <inputs>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
132 <conditional name="singlePaired">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
133 <param name="sPaired" type="select" label="What is the library type?">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
134 <option value="single">Single-end</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
135 <option value="paired">Paired-end</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
136 <option value="collections">Paired-end Collections</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
137 </param>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
138 <when value="single">
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
139 <param name="sInput1" type="data" format="@INPUT_TYPES@" label="Single end illumina fastq file" optional="false"/>
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
140 </when>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
141 <when value="paired">
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
142 <param name="pInput1" type="data" format="@INPUT_TYPES@" label="Forward FASTQ file" help="Must have ASCII encoded quality scores"/>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
143 <param name="pInput2" type="data" format="@INPUT_TYPES@" label="Reverse FASTQ file" help="File format must match the Forward FASTQ file"/>
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
144 <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
145 <option value="pe">Illumina paired-end (short inserts)</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
146 <option value="mp">Illumina mate-pair library (long inserts)</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
147 <option value="pp">Mate-pair sequenced on the same strand</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
148 </param>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
149 </when>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
150 <when value="collections">
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
151 <param name="fastq_collection" type="data_collection" label="Paired-end Fastq collection" help="" optional="false" format="@INPUT_TYPES@" collection_type="paired" />
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
152 <param name="pairtype" type="select" label="Pair Type" help="Type of read pair library">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
153 <option value="pe">Illumina paired-end (short inserts)</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
154 <option value="mp">Illumina mate-pair library (long inserts)</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
155 <option value="pp">Mate-pair sequenced on the same strand</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
156 </param>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
157 </when>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
158
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
159 </conditional>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
160
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
161
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
162
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
163 <!-- reference genome -->
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
164 <param name="reference" type="data" format="fasta" label="Select fasta reference"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
165 <param name="k" type="integer" value="13" label="K-mer size" help="Specifies the word length. [wordlen] is an integer within the limits. between 3 and 20. The default word length is 13" max="20" min="3"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
166 <param name="s" type="integer" optional="true" label="Step size" help="Specifies how many bases are skipped between indexed words."/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
167
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
168
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
169 <param name="mincover" type="text" label="Mincover" help="Only consider mappings where the k-mer word seeds cover the query read to a minimum extent"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
170 <param name="scordiff" type="text" label="Scordiff" help="Set a threshold of the Smith-Waterman alignment score relative to the maximum score"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
171 <conditional name="oformat">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
172 <param name="outformat" type="select" label="Format" help="">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
173 <option value="cigar">cigar</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
174 <option value="sam" selected="true">sam</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
175 <option value="ssaha">ssaha</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
176 <option value="bam">bam</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
177 </param>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
178 <when value="sam">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
179 <param name="samOptions" type="select" display="checkboxes" label="Sam Options" multiple="true">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
180 <option value="nohead">No Header</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
181 <option value="clip">Hard Clip</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
182 </param>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
183 </when>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
184 <when value="bam">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
185 <param name="bamOptions" type="select" display="checkboxes" label="Bam Options" multiple="true">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
186 <option value="clip">Hard Clip</option>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
187 </param>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
188 </when>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
189 <when value="cigar">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
190 </when>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
191 <when value="ssaha">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
192 </when>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
193 </conditional>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
194 <param name="insfil" type="data" optional="true" label="Distribution insert sizes " help="Use the distribution of insert sizes stored in the file [insfil. Thisfile is in ASCII format and can be generated using the 'sample'" format="sam"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
195 <param name="insertmax" type="text" label="Maximum insert size (only in paired-end mode). " help="Maximum insert size (only in paired-end mode). The default is 500."/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
196 <param name="insertmin" type="text" label="Minimum insert size (only in paired-end mode). " help="Minimum insert size (only in paired-end mode). The default is 0."/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
197
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
198
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
199 <param name="minscor" type="text" label="Sets an absolute threshold of the Smith-Waterman scores." help="Mappings with scores below that threshold will not be reported. The default is &#060; minscor &#062; = &#060; wordlen &#062; + &#060; stepsiz &#062; - 1"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
200
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
201 <param name="minbasq" type="text" label="Sets a base quality threshold (0 &#060;= minbasq &#060;= 10, default 0)" help="K-mer words of the read with nucleotides that have a base quality below this threshold are not looked up in the hash index."/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
202
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
203 <param name="seed" type="text" label="If the there are multiple mappings with the same best alignment score report one picked at random." help="is an integer >= 0 used to seed the pseudo-random genarator."/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
204
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
205 <param name="sw_weighted" type="boolean" label="Smith-Waterman scores are complexity weighted."/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
206
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
207 <param name="search_harder" type="boolean" label="This flag triggers a more exhaustive search for alignments at the cost of decreased speed" help="In paired-end mode each mate is mapped independently. (By default the mate with fewer hits in the hash index is mapped first and the vicinity is searched for mappings of its mate.)"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
208
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
209 <param name="minid" type="text" label="Sets an identity threshold for a mapping to be reported (default: 0)." help="specifies the number of exactly matching nucleotides either as a positive integer or as a fraction of the read length (&#062;= 1.0)."/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
210 </inputs>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
211
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
212 <outputs>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
213 <data name="output" format="cigar" >
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
214 <change_format>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
215 <when input="oformat.outformat" value="cigar" format="cigar"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
216 <when input="oformat.outformat" value="sam" format="sam"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
217 <when input="oformat.outformat" value="ssaha" format="ssaha"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
218 <when input="oformat.outformat" value="bam" format="bam"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
219 </change_format>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
220 </data>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
221 </outputs>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
222 <tests>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
223 <test>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
224 <param name="sPaired" value="paired"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
225 <param name="pInput1" value="ecoli_1K_1.fq"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
226 <param name="pInput2" value="ecoli_1K_2.fq"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
227 <param name="pairtype" value="pe"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
228 <param name="source" value="history"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
229 <param name="reference" value="contigs.fasta"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
230 <param name="outformat" value="sam"/>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
231 <output name="output">
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
232 <assert_contents>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
233 <has_text text="SN:NODE_1_length_1000_cov_140.620106" />
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
234 </assert_contents>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
235 </output>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
236 </test>
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
237 <test>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
238 <param name="sPaired" value="paired"/>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
239 <param name="pInput1" value="ecoli_1K_1.fq.gz"/>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
240 <param name="pInput2" value="ecoli_1K_2.fq.gz"/>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
241 <param name="pairtype" value="pe"/>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
242 <param name="source" value="history"/>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
243 <param name="reference" value="contigs.fasta"/>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
244 <param name="outformat" value="sam"/>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
245 <output name="output">
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
246 <assert_contents>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
247 <has_text text="SN:NODE_1_length_1000_cov_140.620106" />
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
248 </assert_contents>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
249 </output>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
250 </test>
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
251 </tests>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
252 <help>
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
253
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
254 **What it does**
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
255
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
256 SMALT is a pairwise sequence alignment program for the experimentingcient mapping of DNA sequencing reads onto genomic reference sequences. It uses a combination of short-word hashing and dynamic programming. Most types of sequencing platforms are supported including paired-end sequencing reads.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
257
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
258
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
259 ------
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
260
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
261
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
262 **Know what you are doing**
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
263
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
264 .. class:: warningmark
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
265
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
266 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
267
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
268 .. __: https://www.sanger.ac.uk/tool/smalt-0/
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
269
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
270 ------
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
271
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
272 **Input formats**
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
273
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
274 SMALT accepts files in Sanger FASTQ format (galaxy type *fastqsanger* or *fastqsanger.gz*). Use the FASTQ Groomer to prepare your files.
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
275
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
276 ------
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
277
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
278
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
279 Please cite the website "https://www.sanger.ac.uk/tool/smalt-0/".
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
280
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
281 ------
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
282
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
283
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
284 -a Output explicit alignments along with the mapping coordinates.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
285
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
286 -c &#060;mincover INT&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
287 Only consider mappings where the k-mer word seeds cover the query read to
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
288 a minimum extent. If &#060;mincover&#062; is an integer or floating point &#062; 1.0, at
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
289 least this many bases of the read must be covered by k-mer word seeds. If
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
290 &#060;mincover&#062; is a floating point &#060;= 1.0, it specifies the fraction of the
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
291 query read length that must be covered by k-mer word seeds. This option
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
292 is only valid in conjunction with the '-x' flag.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
293
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
294 -d &#060;scordiff INT&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
295 Set a threshold of the Smith-Waterman alignment score relative to the
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
296 maximum score. When mapping single reads, all alignments are reported
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
297 that have Smith-Waterman scores within &#060;scorediff&#062; of the maximum.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
298 Mappings with lower scores are skipped. If &#060;scorediff&#062; is set to to a
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
299 value &#060; 0, all alignments are printed that have scores above the
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
300 threshold specified with the '-m &#060;minscor&#062;' option.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
301 For paired reads, only a value of 0 is supported. With the option '-d 0'
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
302 all aligments (pairings) with the best score are output. By default
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
303 (without the option '-d 0') single reads/mates with multiple best mappings
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
304 are reported as 'not mapped'.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
305
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
306 -f &#060;ouform STR&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
307 Specifies the output format. &#060;ouform&#062; can be either 'sam'(default),
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
308 'cigar', 'gff' or 'ssaha'. Optional extension 'sam:nohead,x,clip'
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
309 (see manual). Support for BAM format is dependent on additional
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
310 libraries (not installed).
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
311
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
312 -F &#060;inform STR&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
313 Specifies the input format. The only available format is fastq (default).
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
314 Support for BAM and SAM formats (see: samtools.sourceforge.net) depends
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
315 on additional libraries (not installed).
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
316
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
317 -g &#060;insfil STR&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
318 Use the distribution of insert sizes stored in the file &#060;insfil&#062;. This
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
319 file is in ASCII format and can be generated using the 'sample' task see
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
320 'smalt sample -H' for help).
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
321
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
322 -H Print these instructions.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
323
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
324 -i &#060;insert_max INT&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
325 Maximum insert size (only in paired-end mode). The default is 500.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
326
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
327 -j &#060;insert_min INT&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
328 Minimum insert size (only in paired-end mode). The default is 0.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
329
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
330 -l &#060;pairtyp STR&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
331 Type of read pair library. &#060;pairtyp&#062; can be either 'pe', i.e. for
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
332 the Illumina paired-end library for short inserts ( \|&#8212;&#062; &#060;&#8212;\| ). 'mp'
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
333 for the Illumina mate-pair library for long inserts ( &#060;&#8212;\| \|&#8212;&#062; ) or
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
334 'pp' for mates sequenced on the same strand ( \|&#8212;&#062; \|&#8212;&#062; ). 'pe' is the
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
335 default.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
336
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
337 -m &#060;minscor INT&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
338 Sets an absolute threshold of the Smith-Waterman scores. Mappings with
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
339 scores below that threshold will not be reported. The default is
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
340 &#060;minscor&#062; = &#060;wordlen&#062; + &#060;stepsiz&#062; - 1.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
341
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
342 -n &#060;nthreads INT&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
343 Run smalt using mutiple threads. &#060;nthread&#062; is the number of additional
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
344 threads forked. The order of the reads in the input files is not preserved
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
345 for the output unless '-O' is also specified.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
346
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
347 -o &#060;oufilnam STR&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
348 Write mapping output (e.g. SAM lines) to a separate file. If this option
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
349 is not specified, mappings are written to standard output.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
350
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
351 -O Output mappings in the order of the reads in the input files when using
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
352 multiple threads (option '-n &#060;nthreads&#062;').
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
353
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
354
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
355 -p Report partial alignments if they are complementary on the read (split
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
356 reads).
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
357
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
358 -q &#060;minbasq INT&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
359 Sets a base quality threshold (0 &#060;= minbasq &#060;= 10, default 0).
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
360 K-mer words of the read with nucleotides that have a base quality below
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
361 this threshold are not looked up in the hash index.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
362
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
363 -r &#060;seed INT&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
364 If &#060;seed&#062; &#062;= 0 report an alignment selected at random where there are
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
365 multiple mappings with the same best alignment score. With &#060;seed&#062; = 0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
366 (default) a seed is derived from the current calendar time. If &#060;seed&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
367 &#060; 0 reads with multiple best mappings are reported as 'not mapped'.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
368
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
369 -S &#060;scorspec STR&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
370 Specify alignment penalty scores for a match or mismatch (substitution),
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
371 or for opening or extending a gap. &#060;scorspec&#062; is a comma speparated
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
372 list of integer assigments to one or more of the following variables:
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
373 match, subst, gapopen, gapext, i.e. 'gapopen=-5,gapext=-4' (no spaces
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
374 allowed in &#060;scorespec&#062;). Default:'match=1,subst=-2,gapopen=-4,gapext=-3'
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
375
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
376 -w Smith-Waterman scores are complexity weighted.
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
377
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
378 -x This flag triggers a more exhaustive search for alignments at the cost
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
379 of speed. In paired-end mode each mate is mapped independently.(By
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
380 default the mate with fewer hits in the hash index is mapped first and
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
381 the vicinity is searched for mappings of its mate.)
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
382
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
383 -y &#060;minid FLT&#062;
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
384 Sets an identity threshold for a mapping to be reported (default: 0).
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
385 &#060;minid&#062; specifies the number of exactly matching nucleotides either as
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
386 a positive integer or as a fraction of the read length (&#060;= 1.0).
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
387 </help>
1
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
388 <citations>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
389 <citation type="bibtex">
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
390 @misc{smaltcitation,
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
391 author = {Ponstigl, Hannes},
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
392 year = {2010},
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
393 title = {smalt},
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
394 publisher = {Wellcome Trust Sanger Institute, Cambridge, UK},
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
395 journal = {Online},
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
396 url = {https://www.sanger.ac.uk/tool/smalt-0/}
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
397 }</citation>
fae9ec82e10f "planemo upload for repository https://sourceforge.net/projects/smalt/ commit fce2d3ea556a97998a74bf5359e072dc900608d5"
nml
parents: 0
diff changeset
398 </citations>
0
51ad86498414 planemo upload for repository https://sourceforge.net/projects/smalt/ commit dad1050d2043119952eb284fcd089519f28e4255
nml
parents:
diff changeset
399 </tool>