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Migrated tool version 0.1.1 from old tool shed archive to new tool shed repository
author nilshomer
date Tue, 07 Jun 2011 17:12:32 -0400
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1 <tool id="srma_wrapper" name="Re-align with SRMA" version="0.1.1">
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2 <description></description>
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3 <command interpreter="python">
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4 srma_wrapper.py
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5
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6 #if $refGenomeSource.refGenomeSource == "history":
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7 --ref=$refGenomeSource.ownFile
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8 #else:
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9 --ref=$refGenomeSource.ref.value
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10 #end if
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11 --input=$input --output=$output
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12 --params=$params.source_select --fileSource=$refGenomeSource.refGenomeSource
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13 #if $params.source_select == "pre_set":
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14 --offset="None", --minMappingQuality="None", --minAlleleProbability="None", --minAlleleCoverage="None", --range="None", --correctBases="None", --useSequenceQualities="None", --maxHeapSize="None", --fileSource="None", --params="None", --dbkey="None",
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15 #else:
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16 --offset=$params.offset, --minMappingQuality=$params.minMappingQuality, --minAlleleProbability=$params.minAlleleProbability, --minAlleleCoverage=$params.minAlleleCoverage, --range=$params.range, --correctBases=$params.correctBases, --useSequenceQualities=$params.useSequenceQualities, --maxHeapSize=$params.maxHeapSize, --fileSource=$params.fileSource, --params=$params.params, --dbkey=$params.dbkey, #end if
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17 #if $refGenomeSource.refGenomeSource == "history":
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18 --dbkey=$dbkey
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19 #else:
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20 --dbkey="None"
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21 #end if
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22 </command>
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23 <inputs>
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24 <conditional name="refGenomeSource">
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25 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in reference?">
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26 <option value="built-in">Use a built-in reference</option>
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27 <option value="history">Use one from the history</option>
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28 </param>
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29 <when value="built-in">
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30 <param name="ref" type="select" label="Select a reference genome">
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31 <options from_file="srma_ref.loc">
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32 <column name="value" index="1" />
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33 <column name="name" index="0" />
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34 </options>
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35 </param>
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36 </when>
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37 <when value="history">
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38 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
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39 </when>
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40 </conditional>
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41 <param name="input" type="data" format="bam" label="Input BAM file" help="The input BAM file to re-align"/>
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42 <conditional name="params">
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43 <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">
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44 <option value="pre_set">Commonly Used</option>
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45 <option value="full">Full Parameter List</option>
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46 </param>
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47 <when value="pre_set" />
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48 <when value="full">
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49 <param name="offset" type="integer" value="20" label="Offset" help="The alignment offset" />
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50 <param name="minMappingQuality" type="integer" value="0" label="Minimum mapping quality" help="The minimum mapping quality" />
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51 <param name="minAlleleProbability" type="float" value="0.1" label="Minimum allele probability" help="The minimum allele probability conditioned on coverage (for the binomial quantile)." />
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52 <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 " />
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53 <param name="range" type="text" value="null" label="Range" help="A range to examine" />
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54 <param name="correctBases" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Correct bases" help="Correct bases " />
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55 <param name="useSequenceQualities" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Use sequence qualities" help="Use sequence qualities " />
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56 <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" />
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57 </when>
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58 </conditional>
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59 </inputs>
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60 <outputs>
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61 <data format="bam" name="output" />
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62 </outputs>
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63 <help>
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64 **What it does**
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65
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66 SRMA is a short read micro re-aligner for next-generation high throughput sequencing data.
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67
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68 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.
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69
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70 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.
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71
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72 ------
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73
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74 Please cite the website "http://srma.sourceforge.net" as well as:
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75
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76 Homer N, and Nelson SF. SRMA: short read micro re-aligner. 2010.
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77
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78 ------
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79
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80 **Know what you are doing**
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81
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82 .. class:: warningmark
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83
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84 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.
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85
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86 .. __: http://srma.sourceforge.net/
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87
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88 ------
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89
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90 **Input formats**
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91
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92 SRMA accepts a BAM input file.
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93
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94 ------
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95
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96 **Outputs**
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97
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98 The output is in BAM format, see http://samtools.sourceforge.net for more details.
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99
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100 -------
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101
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102 **SRMA settings**
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103
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104 All of the options have a default value. You can change any of them. Most of the options in SRMA have been implemented here.
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105
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106 ------
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107
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108 **SRMA parameter list**
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109
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110 This is an exhaustive list of SRMA options:
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111
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112 For **SRMA**::
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113
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114 INPUT=File
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115 I=File The input SAM or BAM file. Required.
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116
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117 OUTPUT=File
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118 O=File The output SAM or BAM file. Default value: null.
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119
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120 REFERENCE=File
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121 R=File The reference FASTA file. Required.
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122
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123 OFFSET=Integer The alignment offset. Default value: 20. This option can be set to 'null' to clear the
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124 default value.
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125
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126 MIN_MAPQ=Integer The minimum mapping quality. Default value: 0. This option can be set to 'null' to clear
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127 the default value.
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128
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129 MINIMUM_ALLELE_PROBABILITY=Double
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130 The minimum allele probability conditioned on coverage (for the binomial quantile).
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131 Default value: 0.1. This option can be set to 'null' to clear the default value.
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132
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133 MINIMUM_ALLELE_COVERAGE=Integer
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134 The minimum haploid coverage for the consensus. Default value: 3. This option can be set
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135 to 'null' to clear the default value.
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136
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137 RANGE=String A range to examine. Default value: null.
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138
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139 CORRECT_BASES=Boolean Correct bases. Default value: false. This option can be set to 'null' to clear the
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140 default value. Possible values: {true, false}
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141
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142 USE_SEQUENCE_QUALITIES=BooleanUse sequence qualities Default value: true. This option can be set to 'null' to clear the
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143 default value. Possible values: {true, false}
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144
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145 MAX_HEAP_SIZE=Integer The maximum number of nodes on the heap before re-alignment is ignored Default value:
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146 8192. This option can be set to 'null' to clear the default value.
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147
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148 </help>
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149 <code file="srma_wrapper_code.py" />
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150 </tool>