Mercurial > repos > drosofff > msp_sr_bowtie

annotate sRbowtie.xml @ 19:dd5985c5798d draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit c23d8a44b40e7b6fc7f15dae5b23ceb5929c8ace
author drosofff
date Mon, 26 Jun 2017 19:58:13 -0400
parents 9fe34d55bfb0
children ffe2430ef56d
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1 <tool id="bowtieForSmallRNA" name="sRbowtie" version="1.2">
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2 <description>for FASTA small reads</description>
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3 <requirements>
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4 <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>
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5 <requirement type="package" version="1.2">samtools</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if $refGenomeSource.genomeSource == "history":
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9 bowtie-build -f '$refGenomeSource.ownFile' local_index &&
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10 #else:
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11 ln -f -s '$refGenomeSource.index.fields.path' local_index &&
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12 #end if
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13 #if $input.extension == "fasta":
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14 #set format = "-f"
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15 #elif $input.extension == "fastq":
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16 #set format = "-q"
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17 #end if
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19 ## set the method_prefix
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20 #if $method == "RNA":
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21 #set method_prefix = "-v %s -M 1 --best --strata --norc" % (str($v_mismatches))
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22 #elif $method == "unique":
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23 #set method_prefix = "-v %s -m 1" % (str($v_mismatches))
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24 #elif $method == "multiple":
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25 #set method_prefix = "-v %s -M 1 --best --strata" % (str($v_mismatches))
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26 #elif $method == "k_option":
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27 #set method_prefix = "-v %s -k 1 --best" % (str($v_mismatches))
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28 #elif $method == "n_option":
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29 #set method_prefix = "-n %s -M 1 --best" % (str($v_mismatches))
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30 #elif $method == "a_option":
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31 #set method_prefix = "-v %s -a --best" % (str($v_mismatches))
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32 #end if
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34 ## set the extra_output
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35 #if $additional_fasta == "No":
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36 #set extra_output = ""
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37 #elif $additional_fasta == "al":
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38 #set extra_output = " --al %s " % str($aligned)
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39 #elif $additional_fasta == "unal":
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40 #set extra_output = " --un %s " % str($unaligned)
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41 #else:
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42 #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned))
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43 #end if
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44
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45 #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)
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47 ## run the bowtie alignement
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48 #if $output_format == "tabular":
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49 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $extra_output "local_index" $format $input > $output
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50 #elif $output_format == "sam":
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51 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix $extra_output -S "local_index" $format $input > $output
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52 #elif $output_format == "bam":
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53 bowtie -p \${GALAXY_SLOTS:-4} $method_postfix $extra_output -S "local_index" $format $input |samtools view -bS - > $output
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54 #end if
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56 ]]></command>
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57 <inputs>
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58 <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" />
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59 <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">
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60 <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>
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61 <option value="unique">Match unique mappers on DNA reference index</option>
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62 <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>
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63 <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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64 <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>
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65 <option value="a_option">Match and report all valid alignments</option>
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66 </param>
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67 <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select">
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68 <option value="0">0</option>
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69 <option selected="true" value="1">1</option>
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70 <option value="2">2</option>
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71 <option value="3">3</option>
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72 </param>
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73 <conditional name="refGenomeSource">
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74 <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
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75 <option value="indexed">Use a built-in index</option>
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76 <option value="history">Use one from the history</option>
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77 </param>
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78 <when value="indexed">
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79 <param help="if your genome of interest is not listed - contact instance administrator" label="Select a DNA reference index" name="index" type="select">
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80 <options from_data_table="bowtie_indexes">
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81
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82 </options>
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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 format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
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87 </when>
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88 </conditional>
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89 <param 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" label="Select output format" name="output_format" type="select">
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90 <option selected="true" value="tabular">tabular</option>
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91 <option value="sam">sam</option>
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92 <option value="bam">bam</option>
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93 </param>
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94 <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
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95 <option selected="true" value="No">No</option>
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96 <option value="al">aligned</option>
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97 <option value="unal">unaligned</option>
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98 <option value="al_and_unal">both aligned and unaligned</option>
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99 </param>
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100 </inputs>
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101 <outputs>
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102 <data format="tabular" label="Bowtie Output" name="output">
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103 <change_format>
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104 <when format="sam" input="output_format" value="sam" />
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105 <when format="bam" input="output_format" value="bam" />
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106 </change_format>
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107 <actions>
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108 <conditional name="refGenomeSource.genomeSource">
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109 <when value="indexed">
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110 <action name="dbkey" type="metadata">
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111 <option column="1" name="bowtie_indexes" offset="0" type="from_data_table">
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112 <filter column="0" compare="startswith" keep="False" type="param_value" value="#" />
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113 <filter column="0" ref="refGenomeSource.index" type="param_value" />
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114 </option>
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115 </action>
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116 </when>
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117 <when value="history">
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118 <action name="dbkey" type="metadata">
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119 <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" />
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120 </action>
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121 </when>
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122 </conditional>
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123 </actions>
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124 </data>
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125 <data format="fasta" label="Matched reads" name="aligned">
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126 <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter>
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127 </data>
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128 <data format="fasta" label="Unmatched reads" name="unaligned">
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129 <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter>
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130 </data>
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131 </outputs>
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132 <tests>
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133 <test>
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134 <param name="genomeSource" value="history" />
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135 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
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136 <param name="method" value="unique" />
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137 <param ftype="fasta" name="input" value="input.fa" />
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138 <param name="v_mismatches" value="1" />
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139 <param name="output_format" value="bam" />
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140 <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
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141 </test>
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142 <test>
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143 <param name="genomeSource" value="history" />
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144 <param ftype="fasta" name="ownFile" value="297_reference.fa" />
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145 <param name="method" value="unique" />
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146 <param ftype="fastq" name="input" value="input.fastq" />
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147 <param name="v_mismatches" value="1" />
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148 <param name="output_format" value="bam" />
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149 <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
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150 </test>
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151 </tests>
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152 <help>
0
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153
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154 **What it does**
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155
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156 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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157
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158 .. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
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159
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160 A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
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161
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162 However, this Bowtie wrapper tool only takes FASTQ files as inputs.
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163
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164 The sRbowtie wrapper specifically works with short reads FASTA inputs (-v bowtie mode)
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165
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166 ------
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167
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168 **OPTIONS**
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169
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170 .. class:: infomark
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171
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172 This script uses Bowtie to match reads on a reference index.
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173
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174 Depending on the type of matching, different bowtie options are used:
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175
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176 **Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**
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177
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178 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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179
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180 *-v [0,1,2,3] -M 1 --best --strata -p 12 --norc --suppress 2,6,7,8*
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181
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182 **Match unique mappers on DNA reference index**
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183
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184 Match ONLY unique mappers on DNA reference index
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185
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186 *-v [0,1,2,3] -m 1 -p 12 --suppress 6,7,8*
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187
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188 Note that using this option with -v values other than 0 is questionnable...
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189
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190 **Match on DNA, multiple mappers randomly matched at a single position**
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191
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192 Match multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:
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193
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194 *-v [0,1,2,3] -M 1 --best --strata -p 12 --suppress 6,7,8*
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195
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196 **Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**
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197
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198 Match with highest speed, not guaranteeing best hit for speed gain:
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199
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200 *-v [0,1,2,3] -k 1 --best -p 12 --suppress 6,7,8*
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201
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202
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203 -----
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204
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205 **Input formats**
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206
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207 .. class:: warningmark
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208
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209 *The only accepted format for the script is a raw fasta list of reads, clipped from their adapter*
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210
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211 -----
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212
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213 **OUTPUTS**
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214
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215 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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216
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217 Column Description
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218 -------- --------------------------------------------------------
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219 1 FastaID fasta identifier
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220 2 polarity + or - depending whether the match was reported on the forward or reverse strand
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221 3 target name of the matched target
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222 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
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223 5 Seq sequence of the matched Read
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224
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225 If you choose SAM, you will get the output in unordered SAM format.
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226
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227 .. class:: warningmark
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228
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229 if you choose BAM, the output will be in sorted BAM format.
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230 To be viewable in Trackster, several condition must be fulfilled:
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231
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232 .. class:: infomark
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233
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234 Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes
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235
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236 .. class:: infomark
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237
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238 the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.
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239
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240 Please contact the Galaxy instance administrator if your genome is not referenced
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241
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242 **Matched and unmatched fasta reads can be retrieved, for further analyses**
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243
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244 </help>
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245 <citations>
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246 <citation type="doi">10.1186/gb-2009-10-3-r25</citation>
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247 </citations>
0
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248 </tool>