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1 <tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="0.9.0">
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2 <description>Using iterative sRbowtie Alignments</description>
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3 <requirements>
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4 <requirement type='package'>bowtie</requirement>
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5 </requirements>
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6 <parallelism method="basic"></parallelism>
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7 <command interpreter="python"> sRbowtieCascade.py --output $output
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8 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
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9 --mismatch $mismatches
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10 --input
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11 #for $i in $input:
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12 $i
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13 #end for
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14 --label
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15 #for $i in $input:
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16 "$i.name"
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17 #end for
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18 --index
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19 #if $refGenomeSource1.genomeSource == "history":
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20 $refGenomeSource1.ownFile
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21 #else:
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22 $refGenomeSource1.index.fields.path
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23 #end if
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24 #for $i in $AdditionalQueries:
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25 #if $i.refGenomeSource.genomeSource == "history":
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26 $i.refGenomeSource.ownFile
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27 #else:
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28 $i.refGenomeSource.index.fields.path
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29 #end if
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30 #end for
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31 --indexing-flags
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32 $refGenomeSource1.genomeSource
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33 #for $i in $AdditionalQueries:
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34 $i.refGenomeSource.genomeSource
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35 #end for
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36 --indexName
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37 #if $refGenomeSource1.genomeSource == "history":
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38 "$refGenomeSource1.ownFile.name"
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39 #else:
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40 "$refGenomeSource1.index.fields.name"
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41 #end if
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42 #for $i in $AdditionalQueries:
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43 #if $i.refGenomeSource.genomeSource == "history":
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44 "$i.refGenomeSource.ownFile.name"
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45 #else:
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46 "$i.refGenomeSource.index.fields.name"
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47 #end if
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48 #end for
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49 </command>
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50 <inputs>
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51 <param name="input" type="data" format="fasta" label="Input fasta file: reads clipped from their adapter" help="Only with clipped, raw fasta files" multiple="true"/>
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52 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
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53 <option value="0">0</option>
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54 <option value="1" selected="true">1</option>
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55 <option value="2">2</option>
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56 <option value="3">3</option>
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57 </param>
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58 <!-- First bowtie index selection -->
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59 <conditional name="refGenomeSource1">
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60 <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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61 <option value="indexed">Use a built-in index</option>
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62 <option value="history">Use one from the history</option>
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63 </param>
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64 <when value="indexed">
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65 <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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66 <options from_data_table="bowtie_indexes"/>
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67 </param>
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68 </when>
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69 <when value="history">
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70 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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71 </when>
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72 </conditional>
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73 <!-- End of first bowtie index selection -->
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74 <!-- other bowtie index selections -->
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75 <repeat name="AdditionalQueries" title="Additional Alignment Step">
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76 <conditional name="refGenomeSource">
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77 <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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78 <option value="indexed">Use a built-in index</option>
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79 <option value="history">Use one from the history</option>
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80 </param>
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81 <when value="indexed">
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82 <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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83 <options from_data_table="bowtie_indexes"/>
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84 </param>
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85 </when>
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86 <when value="history">
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87 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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88 </when>
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89 </conditional>
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90 </repeat>
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91 <!-- End of other bowtie index selections -->
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92 </inputs>
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93 <outputs>
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94 <data format="tabular" name="output" label="Cascade Annotation Analysis"/>
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95 </outputs>
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96
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97 <test>
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98 </test>
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99
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100 <help>
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101
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102 **Intro**
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103
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104 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.
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105 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
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106 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
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107
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108 Here The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode, with -k 1)
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109
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110 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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111
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112
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113 ------
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114
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115 **What it does**
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116
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117 .. class:: infomark
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118
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119 This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes.
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120
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121 Reads are Matched on DNA references as fast as possible, without taking care of mapping issues
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122
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123 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
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124
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125 unaligned reads at step N are used input for sRbowtie at step N+1
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126
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127 -----
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128
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129 **Input formats**
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130
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131 .. class:: warningmark
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132
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133 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
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134
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135 -----
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136
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137 **OUTPUTS**
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138
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139 **Annotation table**
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140
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141 </help>
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142 </tool>
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