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1 <tool id="sRbowtie_cascade" name="Annotate smRNA datasets" version="1.0.1">
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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" version="0.12.7">bowtie</requirement>
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5 </requirements>
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6 <command interpreter="python"> sRbowtieCascade.py --output $output
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7 --num-threads \${GALAXY_SLOTS:-4} ## number of processors to be handled by bowtie
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8 --mismatch $mismatches
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9 --input
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10 #for $i in $input:
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11 $i
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12 #end for
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13 --label
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14 #for $i in $input:
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15 "$i.name"
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16 #end for
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17 --index
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18 #if $refGenomeSource1.genomeSource == "history":
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19 $refGenomeSource1.ownFile
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20 #else:
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21 $refGenomeSource1.index.fields.path
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22 #end if
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23 #for $i in $AdditionalQueries:
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24 #if $i.refGenomeSource.genomeSource == "history":
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25 $i.refGenomeSource.ownFile
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26 #else:
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27 $i.refGenomeSource.index.fields.path
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28 #end if
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29 #end for
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30 --indexing-flags
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31 $refGenomeSource1.genomeSource
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32 #for $i in $AdditionalQueries:
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33 $i.refGenomeSource.genomeSource
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34 #end for
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35 --indexName
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36 #if $refGenomeSource1.genomeSource == "history":
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37 "$refGenomeSource1.ownFile.name"
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38 #else:
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39 "$refGenomeSource1.index.fields.name"
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40 #end if
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41 #for $i in $AdditionalQueries:
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42 #if $i.refGenomeSource.genomeSource == "history":
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43 "$i.refGenomeSource.ownFile.name"
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44 #else:
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45 "$i.refGenomeSource.index.fields.name"
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46 #end if
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47 #end for
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48 </command>
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49 <inputs>
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50 <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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51 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
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52 <option value="0">0</option>
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53 <option value="1" selected="true">1</option>
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54 <option value="2">2</option>
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55 <option value="3">3</option>
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56 </param>
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57 <!-- First bowtie index selection -->
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58 <conditional name="refGenomeSource1">
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59 <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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60 <option value="indexed">Use a built-in index</option>
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61 <option value="history">Use one from the history</option>
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62 </param>
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63 <when value="indexed">
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64 <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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65 <options from_data_table="bowtie_indexes"/>
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66 </param>
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67 </when>
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68 <when value="history">
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69 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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70 </when>
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71 </conditional>
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72 <!-- End of first bowtie index selection -->
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73 <!-- other bowtie index selections -->
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74 <repeat name="AdditionalQueries" title="Additional Alignment Step">
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75 <conditional name="refGenomeSource">
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76 <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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77 <option value="indexed">Use a built-in index</option>
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78 <option value="history">Use one from the history</option>
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79 </param>
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80 <when value="indexed">
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81 <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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82 <options from_data_table="bowtie_indexes"/>
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83 </param>
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84 </when>
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85 <when value="history">
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86 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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87 </when>
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88 </conditional>
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89 </repeat>
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90 <!-- End of other bowtie index selections -->
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91 </inputs>
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92 <outputs>
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93 <data format="tabular" name="output" label="Cascade Annotation Analysis"/>
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94 </outputs>
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95
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96
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1
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97 <tests>
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98 <test>
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99 <param name="input" value ="sample1.fa,sample2.fa,sample3.fa" ftype="fasta" />
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100 <param name="genomeSource" value="history" />
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101 <param name="ownFile" value ="dmel-2L-r6.04.fasta" ftype="fasta" />
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102 <param name="AdditionalQueries_0|refGenomeSource|genomeSource" value="history"/>
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103 <param name="AdditionalQueries_0|refGenomeSource|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
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104 <param name="AdditionalQueries_1|refGenomeSource|genomeSource" value="history"/>
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105 <param name="AdditionalQueries_1|refGenomeSource|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
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106 <output name="output" ftype="tabular" file="Cascade_Annotation_Analysis.tab" />
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107 </test>
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108 </tests>
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0
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109 <help>
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110
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111 **Intro**
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112
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113 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.
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114 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
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115 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
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116
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117 Here The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode, with -k 1)
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118
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119 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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120
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121
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122 ------
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123
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124 **What it does**
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125
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126 .. class:: infomark
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127
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128 This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes.
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129
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130 Reads are Matched on DNA references as fast as possible, without taking care of mapping issues
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131
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132 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
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133
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134 unaligned reads at step N are used as input for sRbowtie at step N+1
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135
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136 -----
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137
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138 **Input formats**
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139
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140 .. class:: warningmark
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141
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142 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
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143
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144 -----
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145
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146 **OUTPUTS**
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147
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148 **Annotation table**
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149
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150 </help>
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151 </tool>
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