Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4_mapping.xml @ 9:302d13490b23 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.2 preview 1, BAM output
author peterjc
date Thu, 28 Nov 2013 05:07:59 -0500
parents 902f01c1084b
children 7fcabeeca5df
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
1 <tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.2">
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
2 <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
3 <requirements>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
4 <requirement type="binary">mira</requirement>
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
5 <requirement type="binary">miraconvert</requirement>
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
6 <requirement type="package" version="4.0">MIRA</requirement>
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
7 <requirement type="binary">samtools</requirement>
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
8 <requirement type="package" version="0.1.19">samtools</requirement>
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
9 </requirements>
5
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
10 <version_command interpreter="python">mira4.py --version</version_command>
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
11 <command interpreter="python">
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
12 mira4.py "$manifest" "$out_maf" "$out_bam" "$out_fasta" "$out_log"
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
13 </command>
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
14 <stdio>
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
15 <!-- Assume anything other than zero is an error -->
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
16 <exit_code range="1:" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
17 <exit_code range=":-1" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
18 </stdio>
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
19 <inputs>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
20 <param name="job_type" type="select" label="Assembly type">
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
21 <option value="genome">Genome</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
22 <option value="est">EST (transcriptome)</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
23 </param>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
24 <param name="job_quality" type="select" label="Assembly quality grade">
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
25 <option value="accurate">Accurate</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
26 <option value="draft">Draft</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
27 </param>
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
28 <!-- TODO? Allow technology type for references? -->
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
29 <!-- TODO? Allow strain settings for reference(s) and reads? -->
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
30 <!-- TODO? Use a repeat to allow for multi-strain references? -->
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
31 <!-- TODO? Add strain to the mapping read groups? -->
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
32 <param name="references" type="data" format="fasta,fastq,mira" multiple="true" required="true" label="Backbone reference file(s)"
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
33 help="Multiple files allowed, for example one FASTA file per chromosome or plasmid." />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
34 <param name="strain_setup" type="select" label="Strain configuration (reference vs reads)">
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
35 <option value="default">Different strains - mapping reads onto a related reference ('StrainX' vs 'ReferenceStrain')</option>
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
36 <option value="same">Same strain - mapping reads from same reference (all 'StrainX')</option>
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
37 </param>
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
38 <repeat name="read_group" title="Read Group" min="1">
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
39 <param name="technology" type="select" label="Read technology">
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
40 <option value="solexa">Solexa/Illumina</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
41 <option value="sanger">Sanger cappillary sequencing</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
42 <option value="454">Roche 454</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
43 <option value="iontor">Ion Torrent</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
44 <option value="pcbiolq">PacBio low quality (raw)</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
45 <option value="pcbiohq">PacBio high quality (corrected)</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
46 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
47 </param>
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
48 <conditional name="segments">
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
49 <param name="type" type="select" label="Are these paired reads?">
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
50 <option value="paired">Paired reads</option>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
51 <option value="none">Single reads or not relevant (e.g. primer walking with Sanger capillary sequencing)</option>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
52 </param>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
53 <when value="paired">
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
54 <param name="placement" type="select" label="Pairing type (segment placing)">
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
55 <option value="FR">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
56 <option value="RF">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
57 <option value="SB">2---&gt; 1---&gt; (e.g. Roche 454 paired-end libraries or IonTorrent long-mate; see note)</option>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
58 </param>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
59 <param name="naming" type="select" label="Pair naming convention">
7
902f01c1084b Uploaded v0.0.1 preview 7, with mirabait wrapper
peterjc
parents: 6
diff changeset
60 <option value="solexa">Solexa/Illumina (using '/1' and '/2' suffixes, or later Illumina colon system)</option>
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
61 <option value="FR">Forward/Reverse scheme (using '.f*' and '.r*' suffixes)</option>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
62 <option value="tigr">TIGR scheme (using 'TF*' and 'TR*' suffixes)</option>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
63 <option value="sanger">Sanger scheme (see notes)</option>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
64 <option value="stlouis">St. Louis scheme (see notes)</option>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
65 </param>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
66 </when>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
67 <when value="none" /><!-- no further questions -->
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
68 </conditional>
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
69 <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
70 help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
71 </repeat>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
72 </inputs>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
73 <outputs>
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
74 <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" />
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
75 <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)" />
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
76 <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
77 <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" />
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
78 </outputs>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
79 <configfiles>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
80 <configfile name="manifest">
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
81 project = MIRA
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
82 job = mapping,${job_type},${job_quality}
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
83 parameters = -GE:not=1 -NW:cmrnl -DI:trt=/tmp
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
84 ## -GE:not is short for -GENERAL:number_of_threads and using one (1)
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
85 ## can be useful for repeatability of assemblies and bug hunting.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
86 ##
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
87 ## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
88 ## and without this MIRA aborts with read names over 40 characters
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
89 ## due to limitations of some downstream tools.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
90 ##
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
91 ## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
92 ## point to a local hard drive (not something like NFS on network).
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
93
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
94 ##This bar goes into the manifest as a comment line
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
95 #------------------------------------------------------------------------------
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
96
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
97 readgroup
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
98 is_reference
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
99 #if str($strain_setup)=="same"
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
100 strain = StrainX
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
101 #end if
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
102 #for $f in $references
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
103 ##Must now map Galaxy datatypes to MIRA file types...
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
104 #if $f.ext.startswith("fastq")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
105 ##MIRA doesn't like fastqsanger etc, just plain old fastq:
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
106 data = fastq::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
107 #elif $f.ext == "mira"
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
108 ##We're calling *.maf the "mira" format in Galaxy (name space collision)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
109 data = maf::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
110 #elif $f.ext == "fasta"
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
111 ##We're calling MIRA with the file type as "fna" as otherwise it wants quals
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
112 data = fna::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
113 #else
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
114 ##Currently don't expect anything else...
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
115 data = ${f.ext}::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
116 #end if
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
117 #end for
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
118 #for $rg in $read_group
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
119
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
120 ##This bar goes into the manifest as a comment line
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
121 #------------------------------------------------------------------------------
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
122
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
123 readgroup
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
124 technology = ${rg.technology}
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
125 #if str($strain_setup)=="same"
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
126 ##This is perhaps redundant as MIRA defaults to StrainX for the reads:
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
127 strain = StrainX
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
128 #end if
5
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
129 ##Record the segment placement (if any)
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
130 #if str($rg.segments.type) == "paired"
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
131 segmentplacement = ${rg.segments.placement}
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
132 segmentnaming = ${rg.segments.naming}
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
133 #end if
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
134 #if str($rg.segments.type) == "none"
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
135 segmentplacement = ?
5
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
136 #end if
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
137 ##MIRA will accept multiple filenames on one data line, or multiple data lines
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
138 #for $f in $rg.filenames
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
139 ##Must now map Galaxy datatypes to MIRA file types...
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
140 #if $f.ext.startswith("fastq")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
141 ##MIRA doesn't like fastqsanger etc, just plain old fastq:
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
142 data = fastq::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
143 #elif $f.ext == "mira"
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
144 ##We're calling *.maf the "mira" format in Galaxy (name space collision)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
145 data = maf::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
146 #else
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
147 ##Currently don't expect anything else...
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
148 data = ${f.ext}::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
149 #end if
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
150 #end for
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
151 #end for
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
152 </configfile>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
153 </configfiles>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
154 <tests>
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
155 <!-- Deliberately using default read_group.technology value "solexa"
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
156 as then Galaxy's broken <repeat> handling in tests should work... -->
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
157 <!-- Tests currently failing,
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
158 TwillException: more than one form; you must select one (use 'fv') before submitting
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
159 <test>
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
160 <param name="job_type" value="genome" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
161 <param name="job_quality" value="accurate" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
162 <param name="references" value="tvc_contigs.fasta" ftype="fasta" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
163 <param name="strain_setup" value="default" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
164 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
165 <output name="out_fasta" file="tvc_map_same_strain.fasta" ftype="fasta" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
166 </test>
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
167 <test>
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
168 <param name="job_type" value="genome" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
169 <param name="job_quality" value="accurate" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
170 <param name="references" value="tvc_contigs.fasta" ftype="fasta" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
171 <param name="strain_setup" value="same" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
172 <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
173 <output name="out_fasta" file="tvc_map_ref_strain.fasta" ftype="fasta" />
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
174 </test>
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
175 -->
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
176 </tests>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
177 <help>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
178
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
179 **What it does**
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
180
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
181 Runs MIRA v4.0 in mapping mode, collects the output, generates a sorted BAM
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
182 file, and throws away all the temporary files.
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
183
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
184 MIRA is an open source assembly tool capable of handling sequence data from
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
185 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454, Ion Torrent
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
186 and also PacBio).
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
187
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
188 It is particularly suited to small genomes such as bacteria.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
189
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
190
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
191 **Notes on paired reads**
5
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
192
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
193 .. class:: warningmark
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
194
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
195 MIRA uses read naming conventions to identify paired read partners
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
196 (and does not care about their order in the input files). In most cases,
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
197 the Solexa/Illumina setting is fine. For Sanger capillary sequencing,
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
198 you may need to rename your reads to match one of the standard conventions
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
199 supported by MIRA. For Roche 454 or Ion Torrent the appropriate settings
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
200 depend on how the FASTQ file was produced:
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
201
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
202 * If using Roche's ``sffinfo`` or older versions of ``sff_extract``
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
203 to convert SFF files to FASTQ, your reads will probably have the
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
204 ``---&gt; &lt;---`` orientation and use the ``.f`` and ``.r``
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
205 suffixes (FR naming).
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
206
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
207 * If using a recent version of ``sff_extract``, then the ``/1`` and ``/2``
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
208 suffixes are used (Solexa/Illumina style naming) and the original
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
209 ``2---&gt; 1---&gt;`` orientation is preserved.
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
210
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
211 The reason for this is the raw data for Roche 454 and Ion Torrent paired-end
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
212 libraries sequences a circularised fragment such that the raw data begins
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
213 with the end of the fragment, a linker, then the start of the fragment.
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
214 This means both the start and end are sequenced from the same strand, and
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
215 have the orientation ``2---&gt; 1---&gt;``. However, in order to use the data
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
216 with traditional tools expecting Sanger capillary style ``---&gt; &lt;---``
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
217 orientation it was common to reverse complement one of the pair to mimic this.
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
218
5
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
219
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
220 **Citation**
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
221
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
222 If you use this Galaxy tool in work leading to a scientific publication please
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
223 cite the following papers:
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
224
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
225 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
226 Galaxy tools and workflows for sequence analysis with applications
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
227 in molecular plant pathology. PeerJ 1:e167
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
228 http://dx.doi.org/10.7717/peerj.167
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
229
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
230 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
231 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
232 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
233 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
234
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
235 This wrapper is available to install into other Galaxy Instances via the Galaxy
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
236 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
237 </help>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
238 </tool>