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comparison tools/sr_assembly/mira.xml @ 4:117cce3296af

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Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent. The Galaxy wrapper will no longer work with MIRA v3.2.x - if you are still using the old version of MIRA, please continue to use v0.0.2 of the wrapper.
author peterjc
date Wed, 21 Dec 2011 11:33:19 -0500
parents 298f5c1d9521
children 216bf640baaf
comparison
equal deleted inserted replaced
3:298f5c1d9521 4:117cce3296af
1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.2"> 1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.3">
2 <description>Takes Sanger, Roche, and Illumina data</description> 2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
3 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_tcs $out_ace $out_caf $out_wig $out_log 3 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
4 ##Give the wrapper script list of output filenames, then the mira command... 4 ##Give the wrapper script list of output filenames, then the mira command...
5 mira --job=$job_method,$job_type,$job_quality 5 mira --job=$job_method,$job_type,$job_quality
6 6
7 ##Input files 7 ##Input files
8 #if $condBackbone.use == "true": 8 #if $condBackbone.use == "true":
9 ## Can this be linked to job_method as well? If mapping we need the backbone... 9 ## Can this be linked to job_method as well? If mapping we need the backbone...
10 -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename} 10 -SB:lb=1:bft=1 -FN:bbin=${condBackbone.filename}
11 #end if 11 #end if
12 #if $condSanger.use == "true": 12 #if $condSanger.use == "true":
13 Sanger_SETTINGS 13 SANGER_SETTINGS
14 ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead 14 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
15 -LR:lsd=yes
16 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file 15 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
17 -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename} 16 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
18 #end if 17 #end if
19 #if $condRoche.use == "true": 18 #if $condRoche.use == "true":
20 454_SETTINGS 19 454_SETTINGS
21 ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead 20 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
22 -LR:lsd=yes
23 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file 21 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
24 -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename} 22 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
25 #end if 23 #end if
26 #if $condIllumina.use == "true": 24 #if $condIllumina.use == "true":
27 SOLEXA_SETTINGS 25 SOLEXA_SETTINGS
28 ## Not easy to add solexa to --job, so use load_sequence_data(lsd) instead 26 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
29 -LR:lsd=yes -LR:ft=fastq -FN:fgi=${condIllumina.filename} 27 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
30 ##TODO - Look at -LR FASTQ qual offset (fqqo) 28 ##TODO - Look at -LR FASTQ qual offset (fqqo)
31 #end if 29 #end if
32 30 #if $condIonTorrent.use == "true":
31 IONTOR_SETTINGS
32 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
33 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
34 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
35 #end if
33 36
34 ##Output files 37 ##Output files
35 COMMON_SETTINGS 38 COMMON_SETTINGS
36 ##remove_rollover_logs, remove_log_directory 39 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
37 -OUT:rrol=yes -OUT:rld=yes 40 ##Explicitly disable formats we won't use like MAF (reduce IO)
41 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
42 ##remove_rollover_tmps, remove_tmp_directory
43 -OUT:rrot=1:rtd=1
38 44
39 </command> 45 </command>
40 <inputs> 46 <inputs>
41 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> 47 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
42 <option value="denovo">De novo</option> 48 <option value="denovo">De novo</option>
45 <param name="job_type" type="select" label="Assembly type"> 51 <param name="job_type" type="select" label="Assembly type">
46 <option value="genome">Genome</option> 52 <option value="genome">Genome</option>
47 <option value="est">EST (transcriptome)</option> 53 <option value="est">EST (transcriptome)</option>
48 </param> 54 </param>
49 <param name="job_quality" type="select" label="Assembly quality grade"> 55 <param name="job_quality" type="select" label="Assembly quality grade">
50 <option value="normal">Normal</option> 56 <option value="accurate">Accurate</option>
57 <option value="normal">Normal (deprecated)</option>
51 <option value="draft">Draft</option> 58 <option value="draft">Draft</option>
52 <option value="accurate">Accurate</option>
53 </param> 59 </param>
54 <!-- Backbone --> 60 <!-- Backbone -->
55 <conditional name="condBackbone"> 61 <conditional name="condBackbone">
56 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly."> 62 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
57 <option value="false">No</option> 63 <option value="false">No</option>
80 <option value="false">No</option> 86 <option value="false">No</option>
81 <option value="true">Yes</option> 87 <option value="true">Yes</option>
82 </param> 88 </param>
83 <when value="false" /> 89 <when value="false" />
84 <when value="true"> 90 <when value="true">
85 <param name="filename" type="data" format="fastq,sff" label="Roche 454 reads file" help="FASTQ format" /> 91 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
92 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
86 </when> 93 </when>
87 </conditional> 94 </conditional>
88 <!-- Illumina --> 95 <!-- Illumina -->
89 <conditional name="condIllumina"> 96 <conditional name="condIllumina">
90 <param name="use" type="select" label="Solexa/Illumina reads?"> 97 <param name="use" type="select" label="Solexa/Illumina reads?">
94 <when value="false" /> 101 <when value="false" />
95 <when value="true"> 102 <when value="true">
96 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" /> 103 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
97 </when> 104 </when>
98 </conditional> 105 </conditional>
106 <!-- Ion Torrent -->
107 <conditional name="condIonTorrent">
108 <param name="use" type="select" label="Ion Torrent reads?">
109 <option value="false">No</option>
110 <option value="true">Yes</option>
111 </param>
112 <when value="false" />
113 <when value="true">
114 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
115 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
116 </when>
117 </conditional>
99 </inputs> 118 </inputs>
100 <outputs> 119 <outputs>
101 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> 120 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
102 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> 121 <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)" /> 122 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
105 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> 123 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
106 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> 124 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
107 <data name="out_log" format="txt" label="MIRA log" /> 125 <data name="out_log" format="txt" label="MIRA log" />
108 </outputs> 126 </outputs>
115 133
116 **What it does** 134 **What it does**
117 135
118 Runs MIRA v3, collects the output, and throws away all the temporary files. 136 Runs MIRA v3, collects the output, and throws away all the temporary files.
119 137
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** 138 **Citation**
124 139
125 This tool uses MIRA. If you use this tool in scientific work leading to a 140 This tool uses MIRA. If you use this tool in scientific work leading to a
126 publication, please cite: 141 publication, please cite:
127 142