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comparison tools/sr_assembly/mira.xml @ 1:c947750f82fb draft

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Uploaded v0.0.5
author peterjc
date Wed, 24 Apr 2013 11:51:50 -0400
parents d0a5acdf1638
children 8bddbb4b2575
comparison
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0:d0a5acdf1638 1:c947750f82fb
1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.1"> 1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.5">
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 <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 $out_log
4 ##Give the wrapper script list of output filenames, then the mira command... 5 ##Give the wrapper script list of output filenames, then the mira command...
5 mira --job=$job_method,$job_type,$job_quality 6 mira --job=$job_method,$job_type,$job_quality
6 7
7 ##Input files 8 ##Input files
8 #if $condBackbone.use == "true": 9 #if $condBackbone.use == "true":
9 ## Can this be linked to job_method as well? If mapping we need the backbone... 10 ## Can this be linked to job_method as well? If mapping we need the backbone...
10 -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename} 11 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
11 #end if 12 #end if
12 #if $condSanger.use == "true": 13 #if $condSanger.use == "true":
13 Sanger_SETTINGS 14 SANGER_SETTINGS
14 ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead 15 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
15 -LR:lsd=yes
16 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file 16 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
17 -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename} 17 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
18 #end if 18 #end if
19 #if $condRoche.use == "true": 19 #if $condRoche.use == "true":
20 454_SETTINGS 20 454_SETTINGS
21 ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead 21 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
22 -LR:lsd=yes
23 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file 22 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
24 -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename} 23 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
25 #end if 24 #end if
26 #if $condIllumina.use == "true": 25 #if $condIllumina.use == "true":
27 SOLEXA_SETTINGS 26 SOLEXA_SETTINGS
28 ## Not easy to add solexa to --job, so use load_sequence_data(lsd) instead 27 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
29 -LR:lsd=yes -LR:ft=fastq -FN:fgi=${condIllumina.filename} 28 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
30 ##TODO - Look at -LR FASTQ qual offset (fqqo) 29 ##TODO - Look at -LR FASTQ qual offset (fqqo)
31 #end if 30 #end if
32 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
33 37
34 ##Output files 38 ##Output files
35 COMMON_SETTINGS 39 COMMON_SETTINGS
36 ##remove_rollover_logs, remove_log_directory 40 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
37 -OUT:rrol=yes -OUT:rld=yes 41 ##Explicitly disable formats we won't use like MAF (reduce IO)
42 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
43 ##remove_rollover_tmps, remove_tmp_directory
44 -OUT:rrot=1:rtd=1
38 45
39 </command> 46 </command>
40 <inputs> 47 <inputs>
41 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> 48 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
42 <option value="denovo">De novo</option> 49 <option value="denovo">De novo</option>
45 <param name="job_type" type="select" label="Assembly type"> 52 <param name="job_type" type="select" label="Assembly type">
46 <option value="genome">Genome</option> 53 <option value="genome">Genome</option>
47 <option value="est">EST (transcriptome)</option> 54 <option value="est">EST (transcriptome)</option>
48 </param> 55 </param>
49 <param name="job_quality" type="select" label="Assembly quality grade"> 56 <param name="job_quality" type="select" label="Assembly quality grade">
50 <option value="normal">Normal</option> 57 <option value="accurate">Accurate</option>
58 <option value="normal">Normal (deprecated)</option>
51 <option value="draft">Draft</option> 59 <option value="draft">Draft</option>
52 <option value="accurate">Accurate</option>
53 </param> 60 </param>
54 <!-- Backbone --> 61 <!-- Backbone -->
55 <conditional name="condBackbone"> 62 <conditional name="condBackbone">
56 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly."> 63 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
57 <option value="false">No</option> 64 <option value="false">No</option>
80 <option value="false">No</option> 87 <option value="false">No</option>
81 <option value="true">Yes</option> 88 <option value="true">Yes</option>
82 </param> 89 </param>
83 <when value="false" /> 90 <when value="false" />
84 <when value="true"> 91 <when value="true">
85 <param name="filename" type="data" format="fastq,sff" label="Roche 454 reads file" help="FASTQ format" /> 92 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
93 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
86 </when> 94 </when>
87 </conditional> 95 </conditional>
88 <!-- Illumina --> 96 <!-- Illumina -->
89 <conditional name="condIllumina"> 97 <conditional name="condIllumina">
90 <param name="use" type="select" label="Solexa/Illumina reads?"> 98 <param name="use" type="select" label="Solexa/Illumina reads?">
94 <when value="false" /> 102 <when value="false" />
95 <when value="true"> 103 <when value="true">
96 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" /> 104 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
97 </when> 105 </when>
98 </conditional> 106 </conditional>
107 <!-- Ion Torrent -->
108 <conditional name="condIonTorrent">
109 <param name="use" type="select" label="Ion Torrent reads?">
110 <option value="false">No</option>
111 <option value="true">Yes</option>
112 </param>
113 <when value="false" />
114 <when value="true">
115 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
116 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
117 </when>
118 </conditional>
99 </inputs> 119 </inputs>
100 <outputs> 120 <outputs>
101 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> 121 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
102 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> 122 <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)" /> 123 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
105 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> 124 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
106 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> 125 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
107 <data name="out_log" format="txt" label="MIRA log" /> 126 <data name="out_log" format="txt" label="MIRA log" />
108 </outputs> 127 </outputs>
115 134
116 **What it does** 135 **What it does**
117 136
118 Runs MIRA v3, collects the output, and throws away all the temporary files. 137 Runs MIRA v3, collects the output, and throws away all the temporary files.
119 138
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** 139 **Citation**
124 140
125 This tool uses MIRA. If you use this tool in scientific work leading to a 141 This tool uses MIRA. If you use this tool in scientific work leading to a
126 publication, please cite: 142 publication, please cite:
127 143