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comparison tools/sr_mapping/srma_wrapper.xml @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="srma_wrapper" name="Re-align with SRMA" version="0.2.5">
2 <description></description>
3 <command interpreter="python">srma_wrapper.py
4 #if $refGenomeSource.refGenomeSource_type == "history":
5 --ref=$refGenomeSource.ownFile
6 #else:
7 --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.ref ), $__app__.tool_data_tables[ 'srma_indexes' ].get_fields() )[0][-1] }"
8 --refUID=$refGenomeSource.ref
9 --refLocations=${GALAXY_DATA_INDEX_DIR}/srma_index.loc
10 #end if
11 --input=$input
12 --inputIndex=${input.metadata.bam_index}
13 --output=$output
14 --params=$params.source_select
15 --fileSource=$refGenomeSource.refGenomeSource_type
16 --jarBin="${GALAXY_DATA_INDEX_DIR}/shared/jars"
17 #if $params.source_select == "full":
18 --offset=$params.offset
19 --minMappingQuality=$params.minMappingQuality
20 --minAlleleProbability=$params.minAlleleProbability
21 --minAlleleCoverage=$params.minAlleleCoverage
22 --range=$params.range
23 --correctBases=$params.correctBases
24 --useSequenceQualities=$params.useSequenceQualities
25 --maxHeapSize=$params.maxHeapSize
26 #end if
27 --jarFile="srma.jar"
28 </command>
29 <inputs>
30 <conditional name="refGenomeSource">
31 <param name="refGenomeSource_type" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
32 <option value="built-in">Use a built-in reference</option>
33 <option value="history">Use one from the history</option>
34 </param>
35 <when value="built-in">
36 <param name="ref" type="select" label="Select a reference genome">
37 <options from_data_table="srma_indexes">
38 <filter type="sort_by" column="2" />
39 <validator type="no_options" message="No indexes are available" />
40 </options>
41 </param>
42 </when>
43 <when value="history">
44 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
45 </when>
46 </conditional>
47 <param name="input" type="data" format="bam" label="Input BAM file" help="The input BAM file to re-align"/>
48 <conditional name="params">
49 <param name="source_select" type="select" label="SRMA settings to use" help="For most re-alignment needs, use Commonly Used settings. If you want full control use Full Parameter List">
50 <option value="pre_set">Commonly Used</option>
51 <option value="full">Full Parameter List</option>
52 </param>
53 <when value="pre_set" />
54 <when value="full">
55 <param name="offset" type="integer" value="20" label="Offset" help="The alignment offset" />
56 <param name="minMappingQuality" type="integer" value="0" label="Minimum mapping quality" help="The minimum mapping quality" />
57 <param name="minAlleleProbability" type="float" value="0.1" label="Minimum allele probability" help="The minimum allele probability conditioned on coverage (for the binomial quantile)." />
58 <param name="minAlleleCoverage" type="integer" value="2" label="Minimum allele coverage" help="The minimum haploid coverage for the consensus. Default value: 3. This option can be set " />
59 <param name="range" type="text" value="null" label="Range" help="A range to examine" />
60 <param name="correctBases" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Correct bases" help="Correct bases " />
61 <param name="useSequenceQualities" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Use sequence qualities" help="Use sequence qualities " />
62 <param name="maxHeapSize" type="integer" value="8192" label="Maximum heap size" help="The maximum number of nodes on the heap before re-alignment is ignored" />
63 </when>
64 </conditional>
65 </inputs>
66 <outputs>
67 <data format="bam" name="output" label="${tool.name} on ${on_string}: re-aligned reads">
68 <actions>
69 <conditional name="refGenomeSource.refGenomeSource_type">
70 <when value="built-in">
71 <action type="metadata" name="dbkey">
72 <option type="from_data_table" name="srma_indexes" column="1" offset="0">
73 <filter type="param_value" column="0" value="#" compare="startswith" keep="False" />
74 <filter type="param_value" ref="refGenomeSource.ref" column="0" />
75 </option>
76 </action>
77 </when>
78 <when value="history">
79 <action type="metadata" name="dbkey">
80 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
81 </action>
82 </when>
83 </conditional>
84 </actions>
85 </data>
86 </outputs>
87 <tests>
88 <test>
89 <!-- Commands to run to prepare test files (uses built-in index)
90 Prepare bam index file:
91 samtools index srma_in1.bam
92 Run SRMA:
93 java -jar srma.jar I=srma_in1.bam O=srma_out1.bam R=/afs/bx.psu.edu/depot/data/genome/hg18/srma_index/chr21.fa
94 To create the bam file first, start with a sam file (srma_in1.sam) generated with a run using the chr21 fasta file and which contains the header. Run before samtools index:
95 samtools view -bt /afs/bx.psu.edu/depot/data/genome/hg18/sam_index/chr21.fa -o srma_in1.u.bam srma_in1.sam
96 samtools sort srma_in1.u.bam srma_in1
97 -->
98 <param name="refGenomeSource_type" value="built-in" />
99 <param name="ref" value="hg18chr21" />
100 <param name="input" value="srma_in1.bam" type="bam" />
101 <param name="source_select" value="pre_set" />
102 <output name="output" file="srma_out1.bam" ftype="bam" lines_diff="2" /><!-- allows tag with version number to be different -->
103 </test>
104 <test>
105 <!-- Commands to run to prepare test files (uses custom genome):
106 Prepare custom dict/index files:
107 samtools faidx srma_in2.fa
108 java -cp srma.jar net.sf.picard.sam.CreateSequenceDictionary R=srma_in2.fa O=srma_in2.dict
109 Prepare bam index file:
110 samtools index srma_in3.bam
111 Run SRMA:
112 java -jar "srma.jar" I=srma_in3.bam O=srma_out2.bam R=srma_in2.fa OFFSET=20 MIN_MAPQ=0 MINIMUM_ALLELE_PROBABILITY=0.1 MINIMUM_ALLELE_COVERAGE=2 RANGES=null RANGE=null CORRECT_BASES=true USE_SEQUENCE_QUALITIES=true MAX_HEAP_SIZE=8192
113 To create the bam file first, the sam file needs to have been run with the same reference file (srma_in2.fa) and have the header present. For instance:
114 samtools view -bT srma_in2.fa -o srma_in3.u.bam srma_in3.sam
115 samtools sort srma_in3.u.bam srma_in3
116 -->
117 <param name="refGenomeSource_type" value="history" />
118 <param name="ownFile" value="srma_in2.fa" ftype="fasta" />
119 <param name="input" value="srma_in3.bam" ftype="bam" />
120 <param name="source_select" value="full" />
121 <param name="offset" value="20" />
122 <param name="minMappingQuality" value="0" />
123 <param name="minAlleleProbability" value="0.1" />
124 <param name="minAlleleCoverage" value="2" />
125 <param name="range" value="null" />
126 <param name="correctBases" value="true" />
127 <param name="useSequenceQualities" value="true" />
128 <param name="maxHeapSize" value="8192" />
129 <output name="output" file="srma_out2.bam" ftype="bam" lines_diff="2" /><!-- allows tag with version number to be different -->
130 </test>
131 </tests>
132 <help>
133 **What it does**
134
135 SRMA is a short read micro re-aligner for next-generation high throughput sequencing data.
136
137 Sequence alignment algorithms examine each read independently. When indels occur towards the ends of reads, the alignment can lead to false SNPs as well as improperly placed indels. This tool aims to perform a re-alignment of each read to a graphical representation of all alignments within a local region to provide a better overall base-resolution consensus.
138
139 Currently this tool works well with and has been tested on 30x diploid coverage genome sequencing data from Illumina and ABI SOLiD technology. This tool may not work well with 454 data, as indels are a significant error mode for 454 data.
140
141 ------
142
143 Please cite the website "http://srma.sourceforge.net" as well as:
144
145 Homer N, and Nelson SF. SRMA: short read micro re-aligner. 2010.
146
147 ------
148
149 **Know what you are doing**
150
151 .. class:: warningmark
152
153 There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
154
155 .. __: http://srma.sourceforge.net/
156
157 ------
158
159 **Input formats**
160
161 SRMA accepts a BAM input file. Note that this file should have been generated from a SAM file which contains the header.
162
163 ------
164
165 **Outputs**
166
167 The output is in BAM format, see http://samtools.sourceforge.net for more details.
168
169 -------
170
171 **SRMA settings**
172
173 All of the options have a default value. You can change any of them. Most of the options in SRMA have been implemented here.
174
175 ------
176
177 **SRMA parameter list**
178
179 This is an exhaustive list of SRMA options:
180
181 For **SRMA**::
182
183 INPUT=File
184 I=File The input SAM or BAM file. Required.
185
186 OUTPUT=File
187 O=File The output SAM or BAM file. Default value: null.
188
189 REFERENCE=File
190 R=File The reference FASTA file. Required.
191
192 OFFSET=Integer The alignment offset. Default value: 20. This option can be set to 'null' to clear the
193 default value.
194
195 MIN_MAPQ=Integer The minimum mapping quality. Default value: 0. This option can be set to 'null' to clear
196 the default value.
197
198 MINIMUM_ALLELE_PROBABILITY=Double
199 The minimum allele probability conditioned on coverage (for the binomial quantile).
200 Default value: 0.1. This option can be set to 'null' to clear the default value.
201
202 MINIMUM_ALLELE_COVERAGE=Integer
203 The minimum haploid coverage for the consensus. Default value: 3. This option can be set
204 to 'null' to clear the default value.
205
206 RANGE=String A range to examine. Default value: null.
207
208 CORRECT_BASES=Boolean Correct bases. Default value: false. This option can be set to 'null' to clear the
209 default value. Possible values: {true, false}
210
211 USE_SEQUENCE_QUALITIES=BooleanUse sequence qualities Default value: true. This option can be set to 'null' to clear the
212 default value. Possible values: {true, false}
213
214 MAX_HEAP_SIZE=Integer The maximum number of nodes on the heap before re-alignment is ignored Default value:
215 8192. This option can be set to 'null' to clear the default value.
216
217 </help>
218 </tool>