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comparison tools/mira_3_4/mira.xml @ 8:4266cccbb45a draft

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Uploaded v0.0.7 take 2, fixed path in installation
author peterjc
date Wed, 24 Apr 2013 12:43:17 -0400
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7:4d3f94dfb857 8:4266cccbb45a
1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6">
2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
3 <version_command interpreter="python">mira.py -v</version_command>
4 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
5 ##Give the wrapper script list of output filenames, then the mira command...
6 mira --job=$job_method,$job_type,$job_quality
7
8 ##Input files
9 #if $condBackbone.use == "true":
10 ## Can this be linked to job_method as well? If mapping we need the backbone...
11 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
12 #end if
13 #if $condSanger.use == "true":
14 SANGER_SETTINGS
15 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
16 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
17 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
18 #end if
19 #if $condRoche.use == "true":
20 454_SETTINGS
21 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
22 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
23 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
24 #end if
25 #if $condIllumina.use == "true":
26 SOLEXA_SETTINGS
27 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
28 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
29 ##TODO - Look at -LR FASTQ qual offset (fqqo)
30 #end if
31 #if $condIonTorrent.use == "true":
32 IONTOR_SETTINGS
33 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
34 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
35 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
36 #end if
37
38 ##Output files
39 COMMON_SETTINGS
40
41 ##ignore warnings about long read names
42 -MI:somrnl=0
43
44 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
45 ##Explicitly disable formats we won't use like MAF (reduce IO)
46 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
47
48 ##remove_rollover_tmps, remove_tmp_directory
49 -OUT:rrot=1:rtd=1
50
51 ##put mira temp directory on local storage
52 -DI:trt=/tmp
53
54 </command>
55 <inputs>
56 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
57 <option value="denovo">De novo</option>
58 <option value="mapping">Mapping</option>
59 </param>
60 <param name="job_type" type="select" label="Assembly type">
61 <option value="genome">Genome</option>
62 <option value="est">EST (transcriptome)</option>
63 </param>
64 <param name="job_quality" type="select" label="Assembly quality grade">
65 <option value="accurate">Accurate</option>
66 <option value="normal">Normal (deprecated)</option>
67 <option value="draft">Draft</option>
68 </param>
69 <!-- Backbone -->
70 <conditional name="condBackbone">
71 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
72 <option value="false">No</option>
73 <option value="true">Yes</option>
74 </param>
75 <when value="false" />
76 <when value="true">
77 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
78 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
79 </when>
80 </conditional>
81 <!-- Sanger -->
82 <conditional name="condSanger">
83 <param name="use" type="select" label="Sanger/Capillary reads?">
84 <option value="false">No</option>
85 <option value="true">Yes</option>
86 </param>
87 <when value="false" />
88 <when value="true">
89 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
90 </when>
91 </conditional>
92 <!-- Roche 454 -->
93 <conditional name="condRoche">
94 <param name="use" type="select" label="454 reads?">
95 <option value="false">No</option>
96 <option value="true">Yes</option>
97 </param>
98 <when value="false" />
99 <when value="true">
100 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
101 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
102 </when>
103 </conditional>
104 <!-- Illumina -->
105 <conditional name="condIllumina">
106 <param name="use" type="select" label="Solexa/Illumina reads?">
107 <option value="false">No</option>
108 <option value="true">Yes</option>
109 </param>
110 <when value="false" />
111 <when value="true">
112 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
113 </when>
114 </conditional>
115 <!-- Ion Torrent -->
116 <conditional name="condIonTorrent">
117 <param name="use" type="select" label="Ion Torrent reads?">
118 <option value="false">No</option>
119 <option value="true">Yes</option>
120 </param>
121 <when value="false" />
122 <when value="true">
123 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
124 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
125 </when>
126 </conditional>
127 </inputs>
128 <outputs>
129 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
130 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
131 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
132 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
133 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
134 <data name="out_log" format="txt" label="MIRA log" />
135 </outputs>
136 <tests>
137 </tests>
138 <requirements>
139 <requirement type="python-module">Bio</requirement>
140 <requirement type="binary">mira</requirement>
141 </requirements>
142 <help>
143
144 **What it does**
145
146 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
147
148 **Citation**
149
150 If you use this tool in scientific work leading to a publication, please cite:
151
152 Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
153
154 </help>
155 </tool>