Mercurial > repos > artbio > sr_bowtie_dataset_annotation

annotate sr_bowtie_dataset_annotation.xml @ 3:008de522b3ea draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
author artbio
date Sun, 10 Feb 2019 18:31:51 -0500
parents 243ed53cbc0d
children e11f91575af6
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008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.1.0">
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>
3
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5 <requirement type="package" version="1.3.2">r-optparse</requirement>
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6 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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7 <requirement type="package" version="0.4.1">r-scales</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 $refGenomeSource1.ownFile genome 1>/dev/null &&
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12 ln -s -f '$refGenomeSource1.ownFile' genome.fa &&
e7e7785e41d0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 80b49bd722e8ea8d7dba6dcfe538537cd710d2a2
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13 #set index_path = 'genome'
e7e7785e41d0 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 80b49bd722e8ea8d7dba6dcfe538537cd710d2a2
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14 #else:
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15 #set index_path = $refGenomeSource1.index.fields.path
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16 #end if
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17 #if $input.is_of_type('fasta'):
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18 #set format = "-f"
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19 #elif $input.is_of_type('fastq'):
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20 #set format = "-q"
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21 #end if
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22 #if $format == '-f':
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23 input_nbr_read=\$(( \$(wc -l < $input)/2)) &&
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24 #elif $format == '-q':
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25 input_nbr_read=\$(( \$(wc -l < $input)/4)) &&
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26 #end if
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27 #set method_prefix = "-v %s -k 1 --best" % str($mismatches)
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28 bowtie -p \${GALAXY_SLOTS:-4}
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29 $method_prefix
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30 --al matched.fa
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31 --un unmatched.fa
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32 --suppress 6,7,8
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33 $index_path $format '$input' > tabular_bowtie_output.tab &&
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34 genome_aligned=\$(wc -l < matched.fa) &&
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35 genome_aligned=\$(( \$genome_aligned/2)) &&
1
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36 #if $refGenomeSource1.genomeSource == "history":
2
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37 echo -e "$refGenomeSource1.ownFile.name\t\${genome_aligned}\n" > $output &&
1
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38 #else:
2
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39 echo -e "$refGenomeSource1.index.fields.dbkey\t\${genome_aligned}\n" > $output &&
1
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40 #end if
0
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41 #set counter = 0
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42 #for $i in $AdditionalQueries:
1
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43 rm -f genome.fa &&
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44 #set $counter += 1
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45 #if $counter != 1:
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46 #set input = "class_unmatched.fa"
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47 #else:
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48 #set input = "matched.fa"
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49 #end if
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50 touch temp_class_matched.fa temp_class_unmatched.fa &&
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51 bowtie-build -f $i.ownFile genome 1>/dev/null &&
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52 ln -s -f '$i.ownFile' genome.fa &&
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53 #set index_path = 'genome'
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54 bowtie -p \${GALAXY_SLOTS:-4}
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55 $method_prefix
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56 --al temp_class_matched.fa
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57 --un temp_class_unmatched.fa
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58 --suppress 6,7,8
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59 $index_path $format '$input' > tabular_bowtie_output.tab &&
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60 class_aligned=\$(( \$(wc -l < temp_class_matched.fa)/2)) &&
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61 class_unaligned=\$(( \$(wc -l < temp_class_unmatched.fa)/2)) &&
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62 mv temp_class_unmatched.fa class_unmatched.fa &&
2
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63 echo -e "$i.ownFile.name\t\${class_aligned}\n" >> $output &&
0
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64 #end for
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65 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
3
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66 echo -e "Not classified\t\${remaining}\n" >> $output &&
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67 Rscript $__tool_directory__/barplot.r --input $output --barplot $barplot
0
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68 ]]></command>
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69 <inputs>
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70 <param name="input" type="data" format="fasta,fastq" label="Input file: reads clipped from their adapter" help="Only with clipped, raw fasta or fastq files"/>
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71 <param name="mismatches" type="select" label="Number of mismatches allowed" help="specify the number of mismatches allowed during alignments">
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72 <option value="0">0</option>
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73 <option value="1" selected="true">1</option>
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74 <option value="2">2</option>
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75 <option value="3">3</option>
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76 </param>
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77 <!-- First bowtie index selection -->
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78 <conditional name="refGenomeSource1">
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79 <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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80 <option value="indexed">Use a built-in index</option>
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81 <option value="history">Use one from the history</option>
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82 </param>
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83 <when value="indexed">
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84 <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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85 <options from_data_table="bowtie_indexes"/>
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86 </param>
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87 </when>
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88 <when value="history">
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89 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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90 </when>
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91 </conditional>
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92 <!-- End of first bowtie index selection -->
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93 <!-- other bowtie index selections from fasta in history (mandatory) -->
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94 <repeat name="AdditionalQueries" title="Additional Alignment Step">
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95 <param name="ownFile" type="data" format="fasta" label="Select a fasta file, to serve as index reference" />
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96 </repeat>
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97 <!-- End of other bowtie index selections -->
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98 </inputs>
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99 <outputs>
3
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100 <data format="tabular" name="output" label="Cascade Annotation Analysis">
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101 <actions>
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102 <action name="column_names" type="metadata" default="Reference Index,Number of reads" />
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103 </actions>
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104 </data>
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105 <data name="barplot" format="pdf" label="barplot from ${on_string}" />
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106 </outputs>
0
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107 <tests>
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108 <test>
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109 <param name="input" value ="sample1.fa" ftype="fasta" />
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110 <param name="genomeSource" value="history" />
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111 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
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112 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
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113 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
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114 <output name="output" ftype="tabular" file="sample1_output.tab" />
3
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115 <output name="barplot" ftype="pdf" file="sample1_output.pdf" />
0
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116 </test>
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117 <test>
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118 <param name="input" value ="sample.fastq" ftype="fastq" />
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119 <param name="genomeSource" value="history" />
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120 <param name="ownFile" value ="2L-tail.fa" ftype="fasta" />
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121 <param name="AdditionalQueries_0|ownFile" value="dme_miR21_hairpin.fa" ftype="fasta" />
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122 <param name="AdditionalQueries_1|ownFile" value="Ensembl_transposon_set.fa" ftype="fasta" />
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123 <output name="output" ftype="tabular" file="sample_output.tab" />
3
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124 <output name="barplot" ftype="pdf" file="sample_output.pdf" />
0
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125 </test>
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126 </tests>
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127 <help>
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128
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129 **Introduction**
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130
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131 Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient.
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132 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
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133
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134 Here The sRbowtie wrapper specifically works with short reads FASTA or FASTQ inputs
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135 (-v bowtie mode, with -k 1) which has to be clipped from adapter before alignment.
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136
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137 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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138
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139
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140 ------
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141
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142 **What it does**
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143
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144 .. class:: infomark
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145
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146 This script uses the sRbowtie wrapper to iteratively match reads on a reference indexes.
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147 Read that aligned to the first reference are realigned to the second reference.
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148 From this point, unaligned reads are taken as input for alignment to the third reference, etc.
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149
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150
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151 Reads are Matched on DNA references (both strands) as fast as possible, without taking care of mapping issues
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152
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153 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
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154
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155 unaligned reads at step N are used as input for sRbowtie at step N+1
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156
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157 -----
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158
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159 **Input formats**
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160
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161 .. class:: warningmark
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162
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163 *Reads must be clipped from their adapter and provided in a FASTA or FASTQ format*
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164
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165 -----
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167 **OUTPUTS**
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168
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169 **Annotation table in a tabular format**
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170
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171 </help>
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172 </tool>