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comparison segemehl.xml @ 1:df7c7d732d31 draft

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author rnateam
date Wed, 04 Feb 2015 06:52:06 -0500
parents e97db054a88d
children 0da425524259
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0:e97db054a88d 1:df7c7d732d31
2 <description>based short read aligner</description> 2 <description>based short read aligner</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.1.6">segemehl</requirement> 4 <requirement type="package" version="0.1.6">segemehl</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 <![CDATA[
7 ## prepare segemehl index if no reference genome is supplied 8 ## prepare segemehl index if no reference genome is supplied
8 temp_index = `mktemp`; 9 temp_index = `mktemp`;
9 #if $refGenomeSource.genomeSource == "history": 10 #if $refGenomeSource.genomeSource == "history":
10 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome; 11 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome;
11 #else: 12 #else:
12 $temp_index = ${refGenomeSource.index.fields.index_path} 13 #set $temp_index = ${refGenomeSource.index.fields.index_path}
13 #end if 14 #end if
14 15
15 16
16 ## execute segemehl 17 ## execute segemehl
17 segemehl.x 18 segemehl.x
18 19
19 ## number of threads 20 ## number of threads
20 -t "\${GALAXY_SLOTS:-12}" 21 -t "\${GALAXY_SLOTS:-12}"
21 22
22 ## db file path 23 ## db file path
23 -d ${refGenomeSource.index.fields.db_path} 24 -d ${refGenomeSource.index.fields.db_path}
32 $query_list.append('%s' %($fastq.input_query)) 33 $query_list.append('%s' %($fastq.input_query))
33 #end for 34 #end for
34 -q "#echo ' '.join( $query_list )#" 35 -q "#echo ' '.join( $query_list )#"
35 #else 36 #else
36 ## prepare inputs 37 ## prepare inputs
37 38
38 #set $mate1 = list() 39 #set $mate1 = list()
39 #set $mate2 = list() 40 #set $mate2 = list()
40 #for $mate_pair in $library.mate_list: 41 #for $mate_pair in $library.mate_list:
41 $mate1.append( str($mate_pair.first_strand_query) ) 42 $mate1.append( str($mate_pair.first_strand_query) )
42 $mate2.append( str($mate_pair.second_strand_query) ) 43 $mate2.append( str($mate_pair.second_strand_query) )
60 $autoclip 61 $autoclip
61 $hardclip 62 $hardclip
62 $order 63 $order
63 -s 64 -s
64 -o $segemehl_out 65 -o $segemehl_out
66 ]]>
65 </command> 67 </command>
66 <stdio> 68 <stdio>
67 <regex match="Exit forced" 69 <regex match="Exit forced"
68 source="both" 70 source="both"
69 level="fatal" 71 level="fatal"
70 description="Execution halted." /> 72 description="Execution halted." />
71 </stdio> 73 </stdio>
72 <inputs> 74 <inputs>
73 75
74 <conditional name="refGenomeSource"> 76 <conditional name="refGenomeSource">
135 137
136 <outputs> 138 <outputs>
137 <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/> 139 <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/>
138 </outputs> 140 </outputs>
139 <help> 141 <help>
142 <![CDATA[
140 143
141 .. class:: infomark 144 .. class:: infomark
142 145
143 **What it does** 146 **What it does**
144 147
145 Segemehl_ is a short read mapper with gaps. 148 Segemehl_ is a short read mapper with gaps.
146 149
147 Segemehl_ is a software to map short sequencer reads to reference genomes. 150 Segemehl_ is a software to map short sequencer reads to reference genomes.
148 Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. 151 Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions.
149 Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. 152 Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly.
150 segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl_ allows bisulfite sequencing mapping and split read mapping. 153 segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl_ allows bisulfite sequencing mapping and split read mapping.
151 154
152 .. _Segemehl: http://www.bioinf.uni-leipzig.de/Software/segemehl/ 155 .. _Segemehl: http://www.bioinf.uni-leipzig.de/Software/segemehl/
153 156
154 **References**
155 157
156 Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermueller J: "Fast mapping of short sequences with mismatches, insertions and deletions using index structures", PLoS Comput Biol (2009) vol. 5 (9) pp. e1000502 158 ]]>
157 download latest version: 0.1.6 manual: download here new stuff: faster multiple split read mapping bug fixes: bugfixes: increased sensitivity for strand switches changes: - default accuracy now 90% older segemehl indices are still usable. issues: untraceable errors with gcc compiler gcc-4.5. zlib linker problems with some ubuntu versions complaint department: steve bioinf uni leipzig deshapeimage_1_link_0shapeimage_1_link_1
158
159 </help> 159 </help>
160 <citations>
161 <citation type="doi">10.1371/journal.pcbi.1000502</citation>
162 </citations>
160 </tool> 163 </tool>