Mercurial > repos > peterjc > mira4_assembler

annotate tools/mira4/mira4_de_novo.xml @ 18:381aa262c8cb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.0.2 preview 10, override /tmp via environment variable
author peterjc
date Tue, 25 Mar 2014 07:37:50 -0400
parents 5bbaa930d7fa
children 8487d70e82aa
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_de_novo" name="MIRA v4.0 de novo assember" version="0.0.2">
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
2 <description>Takes 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>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
28 <repeat name="read_group" title="Read Group" min="1">
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
29 <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
30 <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
31 <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
32 <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
33 <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
34 <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
35 <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
36 <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option>
15
b0ffe0e7282b Uploaded v0.0.2 preview 7, fixed bash syntax error
peterjc
parents: 14
diff changeset
37 <!-- TODO reference/backbone as an entry here? -->
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
38 </param>
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
39 <conditional name="segments">
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
40 <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
41 <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
42 <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
43 </param>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
44 <when value="paired">
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
45 <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
46 <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
47 <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
48 <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
49 </param>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
50 <!-- min/max validation is done via the <code> tag -->
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
51 <param name="min_size" type="integer" optional="true" min="0" value=""
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
52 label="Minimum size of 'good' DNA templates in the library preparation"
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
53 help="Optional, but if used you must also supply a maximum value." />
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
54 <param name="max_size" type="integer" optional="true" min="0" value=""
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
55 label="Maximum size of 'good' DNA templates in the library preparation"
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
56 help="Optional, but if used you must also supply a minimum value." />
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
57 <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
58 <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
59 <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
60 <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
61 <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
62 <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
63 </param>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
64 </when>
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
65 <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
66 </conditional>
15
b0ffe0e7282b Uploaded v0.0.2 preview 7, fixed bash syntax error
peterjc
parents: 14
diff changeset
67 <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
b0ffe0e7282b Uploaded v0.0.2 preview 7, fixed bash syntax error
peterjc
parents: 14
diff changeset
68 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
69 </repeat>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
70 </inputs>
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
71 <code file="mira4_validator.py" />
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
72 <outputs>
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
73 <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
74 <data name="out_bam" format="bam" label="MIRA de novo assembly (BAM)" />
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
75 <data name="out_maf" format="mira" label="MIRA de novo assembly" />
14
133b863a8a40 Uploaded v0.0.2 preview 6, include some omitted test files.
peterjc
parents: 13
diff changeset
76 <!-- TODO?
133b863a8a40 Uploaded v0.0.2 preview 6, include some omitted test files.
peterjc
parents: 13
diff changeset
77 <data name="out_contigstats" format="tabular" label="MIRA contig stats" />
133b863a8a40 Uploaded v0.0.2 preview 6, include some omitted test files.
peterjc
parents: 13
diff changeset
78 -->
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
79 <data name="out_log" format="txt" label="MIRA de novo log" />
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
80 </outputs>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
81 <configfiles>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
82 <configfile name="manifest">
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
83 project = MIRA
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
84 job = denovo,${job_type},${job_quality}
13
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
85 parameters = -NW:cmrnl=no -DI:trt=/tmp
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
86 ## -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
87 ## can be useful for repeatability of assemblies and bug hunting.
13
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
88 ## This is overriden by the command line -t switch which is easier
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
89 ## to set from within Galaxy.
0
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 ## -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
92 ## 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
93 ## 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
94 ##
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
95 ## -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
96 ## point to a local hard drive (not something like NFS on network).
18
381aa262c8cb Uploaded v0.0.2 preview 10, override /tmp via environment variable
peterjc
parents: 17
diff changeset
97 ## We replace /tmp with an environment variable via mira4.py
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
98
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
99 #for $rg in $read_group
4
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
100
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
101 ##This bar goes into the manifest as a comment line
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
102 #------------------------------------------------------------------------------
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
103
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
104 readgroup
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
105 technology = ${rg.technology}
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
106 ##Record the segment placement (if any)
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
107 #if str($rg.segments.type) == "paired"
13
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
108 segment_placement = ${rg.segments.placement}
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
109 segment_naming = ${rg.segments.naming}
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
110 #if str($rg.segments.min_size) != "" or str($rg.segments.max_size) != ""
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
111 ##If our min/max validation failed I trust MIRA to give an error message...
13
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
112 template_size = $rg.segments.min_size $rg.segments.max_size
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
113 #end if
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
114 #end if
13
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
115 ##if str($rg.segments.type) == "none"
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
116 ##MIRA4 manual says use segment_placement = unknown or ? for unpaired data
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
117 ##but this stopped working in MIRA 4.0 RC5 and 4.0 (final). See:
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
118 ##http://www.freelists.org/post/mira_talk/Unpaired-reads-and-segment-placement--or-unknown
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
119 ##segment_placement = ?
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
120 ##end if
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
121 ##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
122 #for $f in $rg.filenames
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
123 ##Must now map Galaxy datatypes to MIRA file types...
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
124 #if $f.ext.startswith("fastq")
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
125 ##MIRA doesn't like fastqsanger etc, just plain old fastq:
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
126 data = fastq::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
127 #elif $f.ext == "mira"
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
128 ##We're calling *.maf the "mira" format in Galaxy (name space collision)
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
129 data = maf::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
130 #else
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
131 ##MIRA is happy with fasta as name,
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
132 data = ${f.ext}::$f
df86ed992a1b Uploaded preview 4, lots of work on mapping
peterjc
parents: 0
diff changeset
133 #end if
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
134 #end for
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
135 #end for
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
136 </configfile>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
137 </configfiles>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
138 <tests>
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
139 <!-- Tiger mitochondria, selected paired end Illumina reads from SRR639755
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
140 Note we're using just one repeat group, and only the filenames parameter
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
141 within it, so this should work with current test framework limitations:
13
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
142 TODO: Revise example and/or -NW:cac=warn and -NW:acv=80 settings
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
143 MIRA 4.0 complains as coverage is about x93 which is over 80 limit.
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
144 Also MIRA 4.0 gives three contigs as output.
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
145 <test>
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
146 <param name="job_type" value="genome" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
147 <param name="job_quality" value="accurate" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
148 <param name="filenames" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
149 <output name="out_fasta" file="SRR639755_mito_pairs.mira4_de_novo.fasta" ftype="fasta" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
150 </test>
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
151 -->
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
152 <!-- Simple assembly based on MIRA's minidemo/demo4 example
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
153 Note we're using just one repeat group,
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
154 but several parameters with the repeat
17
5bbaa930d7fa Uploaded v0.0.2 preview 9, more functional tests
peterjc
parents: 15
diff changeset
155 -->
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
156 <test>
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
157 <param name="job_type" value="genome" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
158 <param name="job_quality" value="accurate" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
159 <param name="technology" value="sanger" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
160 <param name="type" value="none" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
161 <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
162 <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
17
5bbaa930d7fa Uploaded v0.0.2 preview 9, more functional tests
peterjc
parents: 15
diff changeset
163 <output name="out_bam" file="empty_file.dat" compare="contains" />
5bbaa930d7fa Uploaded v0.0.2 preview 9, more functional tests
peterjc
parents: 15
diff changeset
164 <output name="out_maf" file="empty_file.dat" compare="contains" />
5bbaa930d7fa Uploaded v0.0.2 preview 9, more functional tests
peterjc
parents: 15
diff changeset
165 <output name="out_log" file="empty_file.dat" compare="contains" />
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
166 </test>
17
5bbaa930d7fa Uploaded v0.0.2 preview 9, more functional tests
peterjc
parents: 15
diff changeset
167 <!-- Simple assembly based on MIRA's minidemo/solexa1 example
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
168 Note we're using just one repeat group,
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
169 but two parameters within the repeat (filename, no pairing)
15
b0ffe0e7282b Uploaded v0.0.2 preview 7, fixed bash syntax error
peterjc
parents: 14
diff changeset
170 -->
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
171 <test>
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
172 <param name="job_type" value="genome" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
173 <param name="job_quality" value="accurate" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
174 <param name="type" value="none" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
175 <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
176 <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
13
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
177 <output name="out_bam" file="empty_file.dat" compare="contains" />
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
178 <output name="out_maf" file="empty_file.dat" compare="contains" />
7fcabeeca5df Uploaded v0.0.2 preview 5, fixes for MIRA 4.0 (final), more verbose error if $MIRA4 path wrong
peterjc
parents: 9
diff changeset
179 <output name="out_log" file="empty_file.dat" compare="contains" />
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
180 </test>
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
181 </tests>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
182 <help>
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 **What it does**
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
185
9
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
186 Runs MIRA v4.0 in de novo mode, collects the output, generates a sorted BAM
302d13490b23 Uploaded v0.0.2 preview 1, BAM output
peterjc
parents: 7
diff changeset
187 file, and then 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
188
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
189 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
190 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
191 and also PacBio).
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
192
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
193 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
194
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
195
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
196 **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
197
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
198 .. class:: warningmark
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
199
6
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
200 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
201 (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
202 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
203 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
204 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
205 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
206
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
207 * 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
208 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
209 ``---&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
210 suffixes (FR naming).
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
211
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
212 * 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
213 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
214 ``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
215
626d5cfd01aa Uploaded v0.0.1 preview 6, support for fragment length (using mira4_validator.py)
peterjc
parents: 5
diff changeset
216 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
217 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
218 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
219 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
220 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
221 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
222 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
223
5
ffefb87bd414 Uploaded v0.0.1 preview 5, using MIRA 4.0 RC4, supports segment_placement (pairing type)
peterjc
parents: 4
diff changeset
224
0
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
225 **Citation**
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
226
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
227 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
228 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
229
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
230 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
231 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
232 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
233 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
234
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
235 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
236 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
237 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
238 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
239
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
240 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
241 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
242 </help>
32f693f6e741 Uploaded v0.0.1 preview0, very much a work in progress, primarily checking mira_datatypes dependency
peterjc
parents:
diff changeset
243 </tool>