Mercurial > repos > artbio > sr_bowtie_dataset_annotation

annotate sr_bowtie_dataset_annotation.xml @ 4:e11f91575af6 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
author artbio
date Wed, 20 Mar 2019 07:12:53 -0400
parents 008de522b3ea
children 279fdd92a615
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e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.2.0">
0
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2 <description>by iterative alignments with sRbowtie</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.2">bowtie</requirement>
4
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5 <requirement type="package" version="1.6.0">r-optparse</requirement>
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6 <requirement type="package" version="3.1.0">r-ggplot2</requirement>
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7 <requirement type="package" version="0.8.0">r-ggrepel</requirement>
0
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #if $refGenomeSource1.genomeSource == "history":
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11 bowtie-build -f $refGenomeSource1.ownFile genome 1>/dev/null &&
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12 #set index_path = 'genome'
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13 #else:
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14 #set index_path = $refGenomeSource1.index.fields.path
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15 #end if
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16 #set method_prefix = "-v %s -k 1 --best" % str($mismatches)
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17 #if $input[0].is_of_type('fasta'):
0
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18 #set format = "-f"
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19 #elif $input[0].is_of_type('fastq'):
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20 #set format = "-q"
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21 #end if
4
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22
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23 #for $file in $input:
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24 #set sample=$file.element_identifier
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25 bowtie -p \${GALAXY_SLOTS:-4}
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26 $method_prefix
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27 --al matched.fa
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28 --un unmatched.fa
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29 --suppress 6,7,8
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30 $index_path $format $file > tabular_bowtie_output.tab &&
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31 genome_aligned=\$(wc -l < matched.fa) &&
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32 genome_aligned=\$(( \$genome_aligned/2)) &&
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33 #set counter = 0
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34 #for $i in $AdditionalQueries:
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35 #set $counter += 1
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36 #if $counter != 1:
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37 #set to_align = "class_unmatched.fa"
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38 #else:
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39 #set to_align = "matched.fa"
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40 #end if
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41 bowtie-build -f $i.ownFile subgenome 1>/dev/null &&
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42 touch tmp_class_matched.fa tmp_class_unmatched.fa &&
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43 bowtie -p \${GALAXY_SLOTS:-4}
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44 $method_prefix
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45 --al tmp_class_matched.fa
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46 --un tmp_class_unmatched.fa
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47 --suppress 6,7,8
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48 subgenome $format '$to_align' > tabular_bowtie_output.tab &&
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49 class_aligned=\$(( \$(wc -l < tmp_class_matched.fa)/2)) &&
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50 class_unaligned=\$(( \$(wc -l < tmp_class_unmatched.fa)/2)) &&
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51 echo -e "$sample\t$i.ownFile.name\t\$class_aligned\t\${genome_aligned}" >> $output &&
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52 mv tmp_class_unmatched.fa class_unmatched.fa &&
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53 rm tmp_class_matched.fa &&
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54 #end for
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55 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
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56 echo -e "$sample\tNot classified\t\${remaining}\t\${genome_aligned}" >> $output &&
0
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57 #end for
4
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58
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59
3
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60 Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot
0
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61 ]]></command>
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62 <inputs>
4
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63 <param name="input" type="data" multiple="True" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/>
0
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64 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
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65 <option value="0">0</option>
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66 <option value="1" selected="true">1</option>
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67 <option value="2">2</option>
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68 <option value="3">3</option>
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69 </param>
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70 <!-- First bowtie index selection -->
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71 <conditional name="refGenomeSource1">
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72 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Bowtie Built-ins were indexed using default options">
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73 <option value="indexed">Use a built-in index</option>
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74 <option value="history">Use one from the history</option>
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75 </param>
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76 <when value="indexed">
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77 <param name="index" type="select" label="Select a DNA reference index" help="if your genome of interest is not listed - contact instance administrator">
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78 <options from_data_table="bowtie_indexes"/>
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79 </param>
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80 </when>
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81 <when value="history">
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82 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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83 </when>
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84 </conditional>
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85 <!-- End of first bowtie index selection -->
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86 <!-- other bowtie index selections from fasta in history (mandatory) -->
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87 <repeat name="AdditionalQueries" title="Additional Alignment Step">
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88 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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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>
3
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93 <data format="tabular" name="output" label="Cascade Annotation Analysis">
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94 <actions>
4
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95 <action name="column_names" type="metadata" default="Sample,Reference Index,Number of reads, Total reads" />
3
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96 </actions>
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97 </data>
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98 <data name="barplot" format="pdf" label="barplot from ${on_string}" />
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99 </outputs>
0
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100 <tests>
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101 <test>
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102 <param name="input" value ="sample1.fa" ftype="fasta" />
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103 <param name="genomeSource" value="history" />
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104 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
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105 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
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106 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
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107 <output name="output" ftype="tabular" file="sample1_output.tab" />
4
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108 <output name="barplot" ftype="pdf" file="sample1_output.pdf" compare="sim_size" delta="500"/>
0
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109 </test>
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110 <test>
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111 <param name="input" value ="sample.fastq" ftype="fastq" />
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112 <param name="genomeSource" value="history" />
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113 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
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114 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
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115 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
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116 <output name="output" ftype="tabular" file="sample_output.tab" />
4
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117 <output name="barplot" ftype="pdf" file="sample_output.pdf" compare="sim_size" delta="500"/>
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118 </test>
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119 <test>
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120 <param name="input" value ="sample5.fa,sample4.fa,sample3.fa,sample2.fa,sample1.fa" ftype="fasta" />
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121 <param name="genomeSource" value="history" />
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122 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
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123 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
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124 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
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125 <output name="output" ftype="tabular" file="multisample5_output.tab" />
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126 <output name="barplot" ftype="pdf" file="multisample5_output.pdf" compare="sim_size" delta="500" />
0
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127 </test>
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128 </tests>
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129 <help>
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130
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131 **Introduction**
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132
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133 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.
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134 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
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135
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136 Here The sRbowtie wrapper specifically works with short reads FASTA or FASTQ inputs
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137 (-v bowtie mode, with -k 1) which has to be clipped from adapter before alignment.
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138
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139 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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140
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141
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142 ------
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143
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144 **What it does**
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145
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146 .. class:: infomark
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147
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148 This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes.
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149 Read that aligned to the first reference are realigned to the second reference.
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150 From this point, unaligned reads are taken as input for alignment to the third reference, etc.
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151
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152
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153 Reads are Matched on DNA references (both strands) as fast as possible, without taking care of mapping issues
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154
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155 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
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156
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157 unaligned reads at step N are used as input for sRbowtie at step N+1
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158
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159 -----
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160
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161 **Input formats**
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162
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163 .. class:: warningmark
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165 *Reads must be clipped from their adapter and provided in a FASTA or FASTQ format*
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167 -----
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169 **OUTPUTS**
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171 **Annotation table in a tabular format**
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173 </help>
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174 </tool>