Mercurial > repos > peterjc > mira_assembler

annotate tools/sr_assembly/mira.xml @ 6:3e7eca1f5d04 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
MIRA wrapper v0.0.5 with <version_command> support and check for MIRA V3.4
author peterjc
date Fri, 01 Feb 2013 10:34:21 -0500
parents 216bf640baaf
children 4d3f94dfb857
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
3e7eca1f5d04 MIRA wrapper v0.0.5 with <version_command> support and check for MIRA V3.4
peterjc
parents: 5
diff changeset
1 <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.5">
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
2 <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
6
3e7eca1f5d04 MIRA wrapper v0.0.5 with <version_command> support and check for MIRA V3.4
peterjc
parents: 5
diff changeset
3 <version_command interpreter="python">mira.py -v</version_command>
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
4 <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
5 ##Give the wrapper script list of output filenames, then the mira command...
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
6 mira --job=$job_method,$job_type,$job_quality
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
7
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
8 ##Input files
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
9 #if $condBackbone.use == "true":
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
10 ## Can this be linked to job_method as well? If mapping we need the backbone...
5
216bf640baaf Uploaded v0.0.4 which fixes a problem in v0.0.3 with the backbone arguments.
peterjc
parents: 4
diff changeset
11 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
12 #end if
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
13 #if $condSanger.use == "true":
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
14 SANGER_SETTINGS
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
15 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
17 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
18 #end if
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
19 #if $condRoche.use == "true":
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
20 454_SETTINGS
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
21 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
22 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
23 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
24 #end if
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
25 #if $condIllumina.use == "true":
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
26 SOLEXA_SETTINGS
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
27 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
28 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
29 ##TODO - Look at -LR FASTQ qual offset (fqqo)
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
30 #end if
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
31 #if $condIonTorrent.use == "true":
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
32 IONTOR_SETTINGS
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
33 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
34 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
35 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
36 #end if
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
37
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
38 ##Output files
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
39 COMMON_SETTINGS
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
40 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
41 ##Explicitly disable formats we won't use like MAF (reduce IO)
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
42 -OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
43 ##remove_rollover_tmps, remove_tmp_directory
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
44 -OUT:rrot=1:rtd=1
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
45
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
46 </command>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
47 <inputs>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
48 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
49 <option value="denovo">De novo</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
50 <option value="mapping">Mapping</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
51 </param>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
52 <param name="job_type" type="select" label="Assembly type">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
53 <option value="genome">Genome</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
54 <option value="est">EST (transcriptome)</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
55 </param>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
56 <param name="job_quality" type="select" label="Assembly quality grade">
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
57 <option value="accurate">Accurate</option>
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
58 <option value="normal">Normal (deprecated)</option>
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
59 <option value="draft">Draft</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
60 </param>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
61 <!-- Backbone -->
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
62 <conditional name="condBackbone">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
63 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
64 <option value="false">No</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
65 <option value="true">Yes</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
66 </param>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
67 <when value="false" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
68 <when value="true">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
69 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
70 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
71 </when>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
72 </conditional>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
73 <!-- Sanger -->
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74 <conditional name="condSanger">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75 <param name="use" type="select" label="Sanger/Capillary reads?">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
76 <option value="false">No</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
77 <option value="true">Yes</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
78 </param>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
79 <when value="false" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
80 <when value="true">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
81 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
82 </when>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
83 </conditional>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
84 <!-- Roche 454 -->
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
85 <conditional name="condRoche">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
86 <param name="use" type="select" label="454 reads?">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
87 <option value="false">No</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
88 <option value="true">Yes</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
89 </param>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
90 <when value="false" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
91 <when value="true">
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
92 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
93 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
94 </when>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
95 </conditional>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
96 <!-- Illumina -->
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
97 <conditional name="condIllumina">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
98 <param name="use" type="select" label="Solexa/Illumina reads?">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
99 <option value="false">No</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
100 <option value="true">Yes</option>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
101 </param>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
102 <when value="false" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
103 <when value="true">
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
104 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
105 </when>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
106 </conditional>
4
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
107 <!-- Ion Torrent -->
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
108 <conditional name="condIonTorrent">
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
109 <param name="use" type="select" label="Ion Torrent reads?">
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
110 <option value="false">No</option>
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
111 <option value="true">Yes</option>
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
112 </param>
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
113 <when value="false" />
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
114 <when value="true">
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
115 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
116 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
117 </when>
117cce3296af Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
peterjc
parents: 3
diff changeset
118 </conditional>
0
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
119 </inputs>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
120 <outputs>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
121 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
122 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
123 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
124 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
125 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
126 <data name="out_log" format="txt" label="MIRA log" />
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
127 </outputs>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
128 <tests>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
129 </tests>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
130 <requirements>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
131 <requirement type="python-module">Bio</requirement>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
132 </requirements>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
133 <help>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
134
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
135 **What it does**
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
136
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
137 Runs MIRA v3, collects the output, and throws away all the temporary files.
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
138
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
139 **Citation**
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
140
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
141 This tool uses MIRA. If you use this tool in scientific work leading to a
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
142 publication, please cite:
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
143
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
144 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.
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
145
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
146 </help>
03b240624b5a Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
147 </tool>