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comparison tools/sr_assembly/mira.xml @ 7:4d3f94dfb857 draft

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Uploaded v0.0.6, tell MIRA to use /tmp for temporary files, and ignore long read names (to prevent it aborting).
author peterjc
date Thu, 14 Feb 2013 06:26:32 -0500
parents 3e7eca1f5d04
children
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6:3e7eca1f5d04 7:4d3f94dfb857
1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.5"> 1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6">
2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> 2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
3 <version_command interpreter="python">mira.py -v</version_command> 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 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
5 ##Give the wrapper script list of output filenames, then the mira command... 5 ##Give the wrapper script list of output filenames, then the mira command...
6 mira --job=$job_method,$job_type,$job_quality 6 mira --job=$job_method,$job_type,$job_quality
35 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename} 35 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
36 #end if 36 #end if
37 37
38 ##Output files 38 ##Output files
39 COMMON_SETTINGS 39 COMMON_SETTINGS
40
41 ##ignore warnings about long read names
42 -MI:somrnl=0
43
40 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output 44 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
41 ##Explicitly disable formats we won't use like MAF (reduce IO) 45 ##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 46 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
47
43 ##remove_rollover_tmps, remove_tmp_directory 48 ##remove_rollover_tmps, remove_tmp_directory
44 -OUT:rrot=1:rtd=1 49 -OUT:rrot=1:rtd=1
50
51 ##put mira temp directory on local storage
52 -DI:trt=/tmp
45 53
46 </command> 54 </command>
47 <inputs> 55 <inputs>
48 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> 56 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
49 <option value="denovo">De novo</option> 57 <option value="denovo">De novo</option>
122 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> 130 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
123 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" /> 131 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
124 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> 132 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
125 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> 133 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
126 <data name="out_log" format="txt" label="MIRA log" /> 134 <data name="out_log" format="txt" label="MIRA log" />
127 </outputs> 135 </outputs>
128 <tests> 136 <tests>
129 </tests> 137 </tests>
130 <requirements> 138 <requirements>
131 <requirement type="python-module">Bio</requirement> 139 <requirement type="python-module">Bio</requirement>
140 <requirement type="binary">mira</requirement>
132 </requirements> 141 </requirements>
133 <help> 142 <help>
134 143
135 **What it does** 144 **What it does**
136 145