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1 <tool id="sRbowtie" name="GED bowtie" version="1.0.0">
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2 <description>small RNA oriented</description>
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3 <requirements><requirement type='package'>bowtie</requirement></requirements>
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4 <parallelism method="basic"></parallelism>
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5 <command interpreter="python"> sRbowtie_wrapper.py $input
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6 $method
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7 $v_mismatches
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8 $output_type
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9 $refGenomeSource.genomeSource
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10 ## the very source of the index (indexed or fasta file)
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11 #if $refGenomeSource.genomeSource == "history":
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12 $refGenomeSource.ownFile
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13 #else:
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14 $refGenomeSource.index
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15 #end if
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16 ##
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17 $output
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18 $aligned
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19 $unaligned
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20 </command>
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21 <inputs>
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22 <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files"/>
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23 <!-- which method will be used -->
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24 <param name="method" type="select" label="What kind of matching do you want to do?" help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand">
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25 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
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26 <option value="unique">Match unique mappers on DNA reference index</option>
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27 <option value="multiple" selected="true">Match on DNA, multiple mappers randomly matched at a single position</option>
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28 <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>
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29 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
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30 <option value="a_option">Match and report all valid alignments</option>
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31 </param>
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32
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33 <!-- END of which method will be used -->
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34
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35 <param name="v_mismatches" type="select" label="Number of mismatches allowed" help="specify the -v bowtie option">
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36 <option value="0">0</option>
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37 <option value="1" selected="true">1</option>
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38 <option value="2">2</option>
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39 <option value="3">3</option>
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40 </param>
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41
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42
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43 <!-- nouvel index in dev below -->
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44 <conditional name="refGenomeSource">
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45 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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46 <option value="indexed">Use a built-in index</option>
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47 <option value="history">Use one from the history</option>
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48 </param>
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49
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50 <when value="indexed">
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51 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact GED team">
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52 <options from_data_table="ged_bowtie_indexes"/>
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53 </param>
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54 </when>
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55 <when value="history">
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56 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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57 </when>
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58 </conditional>
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59 <!-- nouvel index input FIN -->
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60 <param name="output_type" type="select" label="Select output format" help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below">
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61 <option value="tabular" select="true">tabular</option>
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62 <option value="sam">sam</option>
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63 <option value="bam">bam</option>
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64 </param>
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65
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66 <param name="additional_fasta" type="select" label="additional fasta output" help="to get aligned and unaligned reads in fasta format">
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67 <option value="No" select="true">No</option>
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68 <option value="al">aligned</option>
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69 <option value="unal">unaligned</option>
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70 <option value="al_and_unal">both aligned and unaligned</option>
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71 </param>
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72
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73 </inputs>
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74 <outputs>
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75 <data format="tabular" name="output" label="Bowtie Output">
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76 <change_format>
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77 <when input="output_type" value="sam" format="sam" />
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78 <when input="output_type" value="bam" format="bam" />
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79 </change_format>
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80 </data>
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81
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82 <data format="fasta" name="aligned" label="Matched reads">
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83 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
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84 </data>
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85 <data format="fasta" name="unaligned" label ="Unmatched reads">
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86 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
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87 </data>
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88 </outputs>
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89
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90 <help>
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91
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92 **What it does**
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93
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94 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
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95
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96 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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97
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98 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
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99
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100 However, this useful Bowtie wrapper tool only takes as inputs FASTQ files.
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101
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102 Our sRbowtie wrapper is intented to work specifically with short reads FASTA inputs and to serve downstream small RNA sequencing analyses
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103
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104 ------
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105
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106 **OPTIONS**
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107
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108 .. class:: infomark
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109
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110 This script uses Bowtie to match reads on a reference index.
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111
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112 Depending on the type of matching, different bowtie options are used:
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113
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114 **Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**
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115
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116 Match on RNA reference, SENSE strand, randomly attributing multiple mapper to target with least mismatches, the polarity column is suppressed in the bowtie tabular report:
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117
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118 *-v [0,1,2,3] -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8*
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119
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120 **Match unique mappers on DNA reference index**
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121
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122 Match ONLY unique mappers on DNA reference index
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123
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124 *-v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8*
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125
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126 Note that using this option with -v values other than 0 is questionnable...
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127
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128 **Match on DNA, multiple mappers randomly matched at a single position**
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129
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130 Match multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:
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131
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132 *-v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8*
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133
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134 **Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**
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135
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136 Match with highest speed, not guaranteeing best hit for speed gain:
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137
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138 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
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139
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140
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141 -----
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142
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143 **Input formats**
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144
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145 .. class:: warningmark
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146
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147 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
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148
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149 -----
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150
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151 **OUTPUTS**
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152
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153 If you choose tabular as the output format, you will obtain the matched reads in standard bowtie output format, having the following columns::
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154
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155 Column Description
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156 -------- --------------------------------------------------------
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157 1 FastaID fasta identifier
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158 2 polarity + or - depending whether the match was reported on the forward or reverse strand
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159 3 target name of the matched target
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160 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
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161 5 Seq sequence of the matched Read
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162
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163 If you choose SAM, you will get the output in unordered SAM format.
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164
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165 .. class:: warningmark
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166
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167 if you choose BAM, the output will be in sorted BAM format.
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168 To be viewable in Trackster, several condition must be fulfilled:
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169
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170 .. class:: infomark
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171
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172 Reads must have been matched to a FULL genome whose chromosome names are compatible with Trackster genome indexes
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173
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174 .. class:: infomark
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175
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176 the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.
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177
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178 Please contact the GED galaxy team is your reference genome is not referenced properly in GED galaxy
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179
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180 **Optionnal matched and unmatched fasta reads can be obtained, for further annotations**
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181
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182 </help>
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183 </tool>
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