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comparison mira_wrapper_v0.0.2.tar.gz/tools/sr_assembly/mira.xml @ 1:e53a79816f5f

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v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
author peterjc
date Thu, 16 Jun 2011 04:44:00 -0400
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1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.2">
2 <description>Takes Sanger, Roche, and Illumina data</description>
3 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_tcs $out_ace $out_caf $out_wig $out_log
4 ##Give the wrapper script list of output filenames, then the mira command...
5 mira --job=$job_method,$job_type,$job_quality
6
7 ##Input files
8 #if $condBackbone.use == "true":
9 ## Can this be linked to job_method as well? If mapping we need the backbone...
10 -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename}
11 #end if
12 #if $condSanger.use == "true":
13 Sanger_SETTINGS
14 ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead
15 -LR:lsd=yes
16 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
17 -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename}
18 #end if
19 #if $condRoche.use == "true":
20 454_SETTINGS
21 ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead
22 -LR:lsd=yes
23 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
24 -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename}
25 #end if
26 #if $condIllumina.use == "true":
27 SOLEXA_SETTINGS
28 ## Not easy to add solexa to --job, so use load_sequence_data(lsd) instead
29 -LR:lsd=yes -LR:ft=fastq -FN:fgi=${condIllumina.filename}
30 ##TODO - Look at -LR FASTQ qual offset (fqqo)
31 #end if
32
33
34 ##Output files
35 COMMON_SETTINGS
36 ##remove_rollover_logs, remove_log_directory
37 -OUT:rrol=yes -OUT:rld=yes
38
39 </command>
40 <inputs>
41 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
42 <option value="denovo">De novo</option>
43 <option value="mapping">Mapping</option>
44 </param>
45 <param name="job_type" type="select" label="Assembly type">
46 <option value="genome">Genome</option>
47 <option value="est">EST (transcriptome)</option>
48 </param>
49 <param name="job_quality" type="select" label="Assembly quality grade">
50 <option value="normal">Normal</option>
51 <option value="draft">Draft</option>
52 <option value="accurate">Accurate</option>
53 </param>
54 <!-- Backbone -->
55 <conditional name="condBackbone">
56 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
57 <option value="false">No</option>
58 <option value="true">Yes</option>
59 </param>
60 <when value="false" />
61 <when value="true">
62 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
63 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
64 </when>
65 </conditional>
66 <!-- Sanger -->
67 <conditional name="condSanger">
68 <param name="use" type="select" label="Sanger/Capillary reads?">
69 <option value="false">No</option>
70 <option value="true">Yes</option>
71 </param>
72 <when value="false" />
73 <when value="true">
74 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
75 </when>
76 </conditional>
77 <!-- Roche 454 -->
78 <conditional name="condRoche">
79 <param name="use" type="select" label="454 reads?">
80 <option value="false">No</option>
81 <option value="true">Yes</option>
82 </param>
83 <when value="false" />
84 <when value="true">
85 <param name="filename" type="data" format="fastq,sff" label="Roche 454 reads file" help="FASTQ format" />
86 </when>
87 </conditional>
88 <!-- Illumina -->
89 <conditional name="condIllumina">
90 <param name="use" type="select" label="Solexa/Illumina reads?">
91 <option value="false">No</option>
92 <option value="true">Yes</option>
93 </param>
94 <when value="false" />
95 <when value="true">
96 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
97 </when>
98 </conditional>
99 </inputs>
100 <outputs>
101 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
102 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
103 <data name="out_tcs" format="tabular" label="MIRA contigs summary" />
104 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
105 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
106 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
107 <data name="out_log" format="txt" label="MIRA log" />
108 </outputs>
109 <tests>
110 </tests>
111 <requirements>
112 <requirement type="python-module">Bio</requirement>
113 </requirements>
114 <help>
115
116 **What it does**
117
118 Runs MIRA v3, collects the output, and throws away all the temporary files.
119
120 The MIRA transposed contig summary (TCS) file is converted into a tabular file for use within Galaxy.
121 This records one line per base per contig, and including things like the base, quality, coverage and any tags.
122
123 **Citation**
124
125 This tool uses MIRA. If you use this tool in scientific work leading to a
126 publication, please cite:
127
128 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.
129
130 </help>
131 </tool>