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comparison tools/mira3/mira.xml @ 10:a2fb1e67bd11 draft

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Uploaded v0.0.9, correct path in dependency installation; renamed folder
author peterjc
date Thu, 30 Jan 2014 13:21:21 -0500
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9:5573d802e431 10:a2fb1e67bd11
1 <tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8">
2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
3 <requirements>
4 <requirement type="binary">mira</requirement>
5 <requirement type="package" version="3.4.1.1">MIRA</requirement>
6 </requirements>
7 <version_command interpreter="python">mira.py -v</version_command>
8 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
9 ##Give the wrapper script list of output filenames, then the mira command...
10 mira --job=$job_method,$job_type,$job_quality
11
12 ##Input files
13 #if $condBackbone.use == "true":
14 ## Can this be linked to job_method as well? If mapping we need the backbone...
15 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
16 #end if
17 #if $condSanger.use == "true":
18 SANGER_SETTINGS
19 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
20 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
21 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
22 #end if
23 #if $condRoche.use == "true":
24 454_SETTINGS
25 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
26 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
27 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
28 #end if
29 #if $condIllumina.use == "true":
30 SOLEXA_SETTINGS
31 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
32 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
33 ##TODO - Look at -LR FASTQ qual offset (fqqo)
34 #end if
35 #if $condIonTorrent.use == "true":
36 IONTOR_SETTINGS
37 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
38 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
39 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
40 #end if
41
42 ##Output files
43 COMMON_SETTINGS
44
45 ##ignore warnings about long read names
46 -MI:somrnl=0
47
48 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
49 ##Explicitly disable formats we won't use like MAF (reduce IO)
50 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
51
52 ##remove_rollover_tmps, remove_tmp_directory
53 -OUT:rrot=1:rtd=1
54
55 ##put mira temp directory on local storage
56 -DI:trt=/tmp
57
58 </command>
59 <inputs>
60 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
61 <option value="denovo">De novo</option>
62 <option value="mapping">Mapping</option>
63 </param>
64 <param name="job_type" type="select" label="Assembly type">
65 <option value="genome">Genome</option>
66 <option value="est">EST (transcriptome)</option>
67 </param>
68 <param name="job_quality" type="select" label="Assembly quality grade">
69 <option value="accurate">Accurate</option>
70 <option value="normal">Normal (deprecated)</option>
71 <option value="draft">Draft</option>
72 </param>
73 <!-- Backbone -->
74 <conditional name="condBackbone">
75 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
76 <option value="false">No</option>
77 <option value="true">Yes</option>
78 </param>
79 <when value="false" />
80 <when value="true">
81 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
82 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
83 </when>
84 </conditional>
85 <!-- Sanger -->
86 <conditional name="condSanger">
87 <param name="use" type="select" label="Sanger/Capillary reads?">
88 <option value="false">No</option>
89 <option value="true">Yes</option>
90 </param>
91 <when value="false" />
92 <when value="true">
93 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
94 </when>
95 </conditional>
96 <!-- Roche 454 -->
97 <conditional name="condRoche">
98 <param name="use" type="select" label="454 reads?">
99 <option value="false">No</option>
100 <option value="true">Yes</option>
101 </param>
102 <when value="false" />
103 <when value="true">
104 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
105 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
106 </when>
107 </conditional>
108 <!-- Illumina -->
109 <conditional name="condIllumina">
110 <param name="use" type="select" label="Solexa/Illumina reads?">
111 <option value="false">No</option>
112 <option value="true">Yes</option>
113 </param>
114 <when value="false" />
115 <when value="true">
116 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
117 </when>
118 </conditional>
119 <!-- Ion Torrent -->
120 <conditional name="condIonTorrent">
121 <param name="use" type="select" label="Ion Torrent reads?">
122 <option value="false">No</option>
123 <option value="true">Yes</option>
124 </param>
125 <when value="false" />
126 <when value="true">
127 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
128 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
129 </when>
130 </conditional>
131 </inputs>
132 <outputs>
133 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
134 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
135 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
136 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
137 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
138 <data name="out_log" format="txt" label="MIRA log" />
139 </outputs>
140 <tests>
141 <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
142 strain data and miraSearchESTSNPs. Here we just assemble it. -->
143 <!--
144 Commenting out test until Galaxy framework is fixed,
145 https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
146 <test>
147 <param name="job_method" value="denovo" />
148 <param name="job_type" value="est" />
149 <param name="job_qual" value="accurate" />
150 <param name="condBackbone.use" value="false" />
151 <param name="condSanger.use" value="true" />
152 <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
153 <param name="condRoche.use" value="false" />
154 <param name="condIllumina.use" value="false" />
155 <param name="condIonTorrent.use" value="false" />
156 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
157 </test>
158 -->
159 </tests>
160 <help>
161
162 **What it does**
163
164 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
165
166 MIRA is an open source assembly tool capable of handling sequence data from
167 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
168 Ion Torrent).
169
170 It is particularly suited to small genomes such as bacteria.
171
172 **Citation**
173
174 If you use this Galaxy tool in work leading to a scientific publication please
175 cite the following papers:
176
177 Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
178 Galaxy tools and workflows for sequence analysis with applications
179 in molecular plant pathology. PeerJ 1:e167
180 http://dx.doi.org/10.7717/peerj.167
181
182 Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
183 Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
184 Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
185 http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
186
187 This wrapper is available to install into other Galaxy Instances via the Galaxy
188 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
189
190 </help>
191 </tool>