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annotate small_rna_maps.xml @ 26:376fae7c9f32 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 32eba59fa52705ae74fd9fe65f6f55be783bfc74
author artbio
date Sun, 14 Apr 2019 14:43:44 -0400
parents 07aa8f928d4b
children fe1a9cfaf5c3
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26
376fae7c9f32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 32eba59fa52705ae74fd9fe65f6f55be783bfc74
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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.13.1">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
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5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
5
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6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
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7 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
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8 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
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9 <requirement type="package" version="1.4.2=r3.3.2_0">r-reshape2</requirement>
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10 <requirement type="package" version="0.6.6">sambamba</requirement>
0
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11 </requirements>
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12 <stdio>
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13 <exit_code range="1:" level="fatal" description="Tool exception" />
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14 </stdio>
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15 <command detect_errors="exit_code"><![CDATA[
22
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16 #import json
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17 #import os
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18 #for $file in $inputs
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19 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' &&
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20 samtools index '$file.element_identifier' &&
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21 #end for
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22 python '$__tool_directory__'/small_rna_maps.py
22
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23 --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }
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24 #set $labels = list()
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25 #for $file in $inputs:
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26 $labels.append(str($file.element_identifier))
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27 #end for
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28 --sample_names ${ ' '.join(['"%s"' % x for x in $labels]) }
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29 --minsize $minsize
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30 --maxsize $maxsize
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31 #if str($plots_options.plots_options_selector ) == "two_plot":
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32 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
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33 --outputs '$output_tab' '$extra_output_tab' &&
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34 #elif str($plots_options.plots_options_selector ) == "global":
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35 --plot_methods 'Size'
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36 --outputs '$output_tab' &&
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37 #elif str($plots_options.plots_options_selector ) == "cluster":
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38 --plot_methods 'Counts'
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39 --outputs '$output_tab'
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40 --cluster ${plots_options.cluster}
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41 --bed '$output_bed'
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42 --bed_skipsize ${plots_options.skip_size}
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43 --bed_skipcounts ${plots_options.skip_counts}
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44 --bed_skipdensity ${plots_options.skip_density}
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45 ${plots_options.strandness} &&
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46 #else:
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47 --plot_methods '${plots_options.first_plot}'
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48 --outputs '$output_tab' &&
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49 #end if
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50
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51
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52 Rscript '$__tool_directory__'/small_rna_maps.r
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53 --first_dataframe '$output_tab'
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54 --extra_dataframe '$extra_output_tab'
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55 #if len(str($normalization)) != 1:
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56 --normalization "${ ' '.join( [factor for factor in $normalization.split()]) }"
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57 #else:
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58 --normalization "${ ' '.join( ["1" for factor in $inputs] )}"
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59 #end if
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60 #if $ylimits_cond.ylimits == "no":
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61 --ymin '' --ymax ''
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62 #else:
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63 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
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64 #end if
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65 #if str($plots_options.plots_options_selector ) == "two_plot":
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66 --first_plot_method '${plots_options.first_plot}'
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67 --extra_plot_method '${plots_options.extra_plot}'
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68 #elif str($plots_options.plots_options_selector ) == "global":
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69 --first_plot_method 'Size'
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70 --extra_plot_method ''
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71 --global '${plots_options.mergestrands}'
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72 #else:
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73 --first_plot_method '${plots_options.first_plot}'
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74 --extra_plot_method ''
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75 #end if
7
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76 --output_pdf '$output_pdf'
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77 ]]></command>
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78 <inputs>
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79 <param name="inputs" type="data" format="bam" label="Select a alignment files to parse" multiple="true"
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80 help="maps from these bam inputs will be collected in a single pdf output" />
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81 <param name="normalization" type="text" label="Enter a size/normalization factor."
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82 help="Enter normalisation factors separated by space eg [0.75 1.23 1.1], no normalization if no values" value="1"/>
8
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83 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
26
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84 value="19" help="default value: 19" />
8
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artbio
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85 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
26
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86 value="29" help="default value: 29" />
5
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parents: 4
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87 <conditional name="plots_options">
7
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88 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
5
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89 <option value="one_plot">Just one plot per chromosome</option>
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90 <option value="two_plot" selected="True">Two plots per chromosome</option>
15
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91 <option value="global">Global read size distributions of aligned reads</option>
16
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92 <option value="cluster">Map read clusters</option>
5
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parents: 4
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93 </param>
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94 <when value="two_plot">
12
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95 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
15
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96 <option value="Counts">Counts</option>
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97 <option value="Coverage">Coverage</option>
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98 <option value="Mean">Mean Sizes</option>
5
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parents: 4
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99 <option value="Median">Median Sizes</option>
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parents: 4
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100 <option value="Size">Size Distributions</option>
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101 </param>
12
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102 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
15
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parents: 14
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103 <option value="Counts">Counts</option>
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parents: 14
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104 <option value="Coverage">Coverage</option>
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105 <option value="Mean">Mean Sizes</option>
5
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parents: 4
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106 <option value="Median">Median Sizes</option>
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107 <option value="Size">Size Distributions</option>
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diff changeset
108 </param>
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109 </when>
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110 <when value="one_plot">
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111 <param name="first_plot" type="select" display="radio" label="select the type of plot">
15
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artbio
parents: 14
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112 <option value="Counts">Counts</option>
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artbio
parents: 14
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113 <option value="Coverage">Coverage</option>
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114 <option value="Mean">Mean Sizes</option>
5
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parents: 4
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115 <option value="Median">Median Sizes</option>
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116 <option value="Size">Size Distributions</option>
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117 </param>
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118 </when>
7
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119 <when value="global">
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120 <param name="first_plot" type="hidden" value="Size"/>
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121 <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram">
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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122 <option value="nomerge">Do not merge</option>
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artbio
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123 <option value="merge">Merge forward and reverse reads</option>
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124 </param>
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125 </when>
16
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artbio
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diff changeset
126 <when value="cluster">
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127 <param name="first_plot" type="hidden" value="Counts"/>
20
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128 <param name="cluster" type="integer" label="Clustering distance in nucleotides" value="1"
16
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129 help="Sets the distance (in nt) below which reads are clustered to a single median position" />
17
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130 <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false"
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131 label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/>
20
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132 <param name="skip_size" type="integer" label="do not report clusters whose size is less than the specified value" value="1"
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133 help="Cluster size threshod (in nucleotides) for reporting. Set to 1 (default) reports all clusters, including singlets" />
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134 <param name="skip_counts" type="integer" label="do not report cluster with a number of reads lower than the specified value" value="1"
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135 help="Number-of-reads threshod (in nucleotides) for cluster reporting. Set to 1 (default) reports all clusters, irrespective of their counts" />
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136 <param name="skip_density" type="float" label="do not report cluster with density equal or less than the specified value" value="0"
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137 help="Density threshod (in reads per nucleotides) for reporting. Set to 0 (default) reports all cluster densities" />
16
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138 </when>
5
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139 </conditional>
12
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140 <conditional name="ylimits_cond">
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141 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
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142 help="This limit won't be applied to size distribution plots"/>
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143 <when value="yes">
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144 <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/>
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145 <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/>
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146 </when>
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147 <when value="no">
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148 </when>
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149 </conditional>
0
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150 </inputs>
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151
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152 <outputs>
7
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153 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
18
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154 <data format="bed" name="output_bed" label="bed file for clusters" >
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155 <filter>plots_options['plots_options_selector'] == 'cluster'</filter>
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156 </data>
7
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157 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
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158 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
15
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diff changeset
159 </data>
7
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160 <data format="pdf" name="output_pdf" label="small RNA maps" />
0
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161 </outputs>
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162
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163 <tests>
17
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artbio
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164 <test> <!-- 0 -->
22
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artbio
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165 <param name="inputs" value="input1.bam,input_new2.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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166 <param name="normalization" value="1 2" />
15
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artbio
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167 <param name="plots_options_selector" value="one_plot" />
82fedc576024 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c1d96f7f028512aa4d8fcae3dd5f967cd445708e
artbio
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168 <param name="first_plot" value="Counts" />
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artbio
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169 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
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artbio
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170 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
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171 </test>
17
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artbio
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172 <test> <!-- 1 -->
22
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173 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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174 <param name="normalization" value="1.0" />
12
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artbio
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175 <param name="ylimits" value="yes" />
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artbio
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176 <param name="ymin" value="-5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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177 <param name="ymax" value="5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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178 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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179 <param name="first_plot" value="Counts" />
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180 <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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181 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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182 </test>
17
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artbio
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183 <test> <!-- 2 -->
22
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artbio
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184 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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185 <param name="normalization" value="1.0" />
17
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186 <param name="plots_options_selector" value="cluster" />
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artbio
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187 <param name="first_plot" value="Counts" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
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188 <param name="cluster" value="5" />
20
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189 <param name="skip_size" value="1" />
17
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190 <param name="strandness" value="false" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
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191 <output file="clustering.tab" name="output_tab" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
artbio
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192 <output file="clustering.pdf" name="output_pdf" />
18
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artbio
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193 <output file="bed1.bed" name="output_bed" />
17
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194 </test>
16
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artbio
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195 <test> <!-- 3 -->
22
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artbio
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196 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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197 <param name="normalization" value="1.0" />
16
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artbio
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198 <param name="plots_options_selector" value="cluster" />
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artbio
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199 <param name="first_plot" value="Counts" />
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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200 <param name="cluster" value="5" />
20
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201 <param name="skip_size" value="1" />
17
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artbio
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202 <param name="strandness" value="true" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
artbio
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203 <output file="clustering_unstranded.tab" name="output_tab" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
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204 <output file="clustering_unstranded.pdf" name="output_pdf" />
18
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205 <output file="bed2.bed" name="output_bed" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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diff changeset
206 </test>
20
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artbio
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207 <test> <!-- 4 -->
22
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artbio
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208 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
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diff changeset
209 <param name="normalization" value="1.0" />
18
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
artbio
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diff changeset
210 <param name="plots_options_selector" value="cluster" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
artbio
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diff changeset
211 <param name="first_plot" value="Counts" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
artbio
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212 <param name="cluster" value="5" />
20
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artbio
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diff changeset
213 <param name="skip_size" value="2" />
18
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artbio
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214 <param name="strandness" value="false" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
artbio
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215 <output file="clustering.tab" name="output_tab" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
artbio
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216 <output file="clustering.pdf" name="output_pdf" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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217 <output file="bed3.bed" name="output_bed" />
12
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218 </test>
20
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219 <test> <!-- 5 -->
22
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artbio
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220 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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221 <param name="normalization" value="1.0" />
20
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222 <param name="plots_options_selector" value="cluster" />
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223 <param name="first_plot" value="Counts" />
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224 <param name="cluster" value="5" />
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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225 <param name="skip_size" value="2" />
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226 <param name="skip_counts" value="3" />
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227 <param name="skip_density" value="1.0" />
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228 <param name="strandness" value="false" />
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229 <output file="clustering.tab" name="output_tab" />
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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230 <output file="clustering.pdf" name="output_pdf" />
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231 <output file="bed4.bed" name="output_bed" />
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232 </test>
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233 <test> <!-- 6 -->
22
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234 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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235 <param name="normalization" value="1.0" />
20
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236 <param name="plots_options_selector" value="cluster" />
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237 <param name="first_plot" value="Counts" />
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238 <param name="cluster" value="5" />
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
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239 <param name="skip_size" value="2" />
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artbio
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240 <param name="skip_counts" value="2" />
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artbio
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241 <param name="skip_density" value="0.4" />
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
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242 <param name="strandness" value="true" />
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243 <output file="clustering_unstranded.tab" name="output_tab" />
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artbio
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244 <output file="clustering_unstranded.pdf" name="output_pdf" />
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245 <output file="bed5.bed" name="output_bed" />
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246 </test>
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247 <test> <!-- 7 -->
22
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248 <param name="inputs" value="input1.bam" ftype="bam" />
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249 <param name="normalization" value="1.0" />
12
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250 <param name="plots_options_selector" value="one_plot" />
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251 <param name="first_plot" value="Size" />
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252 <output file="input1_min20_max30_size.tab" name="output_tab" />
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253 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
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254 </test>
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255 <test> <!-- 8 -->
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256 <param name="inputs" value="input1.bam" ftype="bam" />
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257 <param name="normalization" value="1.0" />
12
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258 <param name="plots_options_selector" value="one_plot" />
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259 <param name="first_plot" value="Mean" />
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260 <output file="input1_mean.tab" name="output_tab" />
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261 <output file="input1__single_plot_mean.pdf" name="output_pdf" />
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262 </test>
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263 <test> <!-- 9 -->
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264 <param name="inputs" value="input1.bam" ftype="bam" />
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265 <param name="normalization" value="1.0" />
12
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266 <param name="plots_options_selector" value="one_plot" />
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267 <param name="first_plot" value="Median" />
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268 <output file="input1_median.tab" name="output_tab" />
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269 <output file="input1_single_plot_median.pdf" name="output_pdf" />
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270 </test>
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271 <test> <!-- 10 -->
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272 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
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273 <param name="normalization" value="1.0 2.0" />
12
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274 <param name="plots_options_selector" value="one_plot" />
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275 <param name="first_plot" value="Counts" />
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276 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
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277 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
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278 </test>
20
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279 <test> <!-- 11 -->
22
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280 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
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281 <param name="normalization" value="1.0 1.0" />
12
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282 <param name="ylimits" value="yes" />
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283 <param name="ymin" value="-5" />
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284 <param name="ymax" value="5" />
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285 <param name="plots_options_selector" value="two_plot" />
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286 <param name="first_plot" value="Counts" />
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287 <param name="extra_plot" value="Size" />
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288 <output file="input1_input2_counts.tab" name="output_tab" />
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289 <output file="input1_input2_size.tab" name="extra_output_tab" />
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290 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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291 </test>
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292 <test> <!-- 12 -->
22
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293 <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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294 <param name="normalization" value="1.0 1.0 1.0 1.0 1.0 1.0" />
9
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295 <param name="plots_options_selector" value="one_plot" />
12
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296 <param name="first_plot" value="Coverage" />
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297 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
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298 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
9
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299 </test>
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300 <test> <!-- 13 -->
22
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301 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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302 <param name="normalization" value="1.0 1.0" />
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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303 <param name="plots_options_selector" value="global" />
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304 <param name="mergestrands" value="nomerge" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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305 <param name="first_plot" value="Size" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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306 <output file="size.tab" name="output_tab" />
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307 <output file="global_nomerge.pdf" name="output_pdf" />
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308 </test>
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309 <test> <!-- 14 -->
22
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310 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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311 <param name="normalization" value="1.0 1.0" />
7
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312 <param name="plots_options_selector" value="global" />
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313 <param name="mergestrands" value="merge" />
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314 <param name="first_plot" value="Size" />
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315 <output file="size.tab" name="output_tab" />
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316 <output file="global_merge.pdf" name="output_pdf" />
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317 </test>
0
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318 </tests>
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319 <help>
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320
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321 **What it does**
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322
23
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diff changeset
323 Plots mapping statistics of read alignments along reference chromosomes or genes or arbitrary regions :
6
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
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324
12
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325 - counts
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326 - mean sizes
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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327 - median sizes
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328 - coverage depth
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329 - size distribution
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330
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331 Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads
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332 in each position of a chromosome reference.
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333 Coverage depths are computed from the input bam alignment files using the python pysam module.
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334
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335 The metrics mentioned above can be plotted either separately:
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336
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337 .. image:: one_plot.png
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338
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339 Or in all possible pairwise combinations:
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340
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341 .. image:: two_plot.png
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342
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343 For comparison purposes, values from bam alignment files can be normalized by a size factor
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344 before plotting (Normalisation field)
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345
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346 *Cluster mode*
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347
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348 Cluster of read alignments are aggregated along regions of *variable* lengths. The Clustering
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349 algorithm works as follows:
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350
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351 A read is clustered with the following read on the genomic reference if the two reads are
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352 separated by at maximum the clustering distance (set in nucleotides). If clustered, the step is
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353 repeated with the following read until clustering fails. A new cluster is then searched.
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354
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355 For clustering procedure, one has the possibility to consider the polarity of reads (only forward
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356 reads or reverse reads can be clustered separately), or to ignore this polarity.
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357
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358 Cluster reads are plotted as for single reads, their coordinate being the median of extrem coordinates of the cluster.
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359
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360 In addition, cluster are reported in a bed file, where clusters can be filtered out upon various parameters,
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361 cluster size, cluster read number or cluster read density (number of reads divided by the length of the cluster).
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362
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363 **Inputs**
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364
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365 bam alignment files that must be
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366
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367 - single-read
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368 - sorted
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369 - mapped to the same reference
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370
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371 .. class:: warningmark
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372
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373 This tools follows a "map-reduce" procedure: multiple inputs, that can be arranged as a data collection,
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374 are visualised side by side in a single pdf file.
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375
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376
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377
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378 **Output**
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379
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380 A pdf file generated by the R package lattice and one or two dataframes used to plot the data.
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381
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382 </help>
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383
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384 <citations>
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385 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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386 <citation type="bibtex">@Book{,
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387 title = {Lattice: Multivariate Data Visualization with R},
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388 author = {Deepayan Sarkar},
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389 publisher = {Springer},
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390 address = {New York},
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391 year = {2008},
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392 note = {ISBN 978-0-387-75968-5},
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393 url = {http://lmdvr.r-forge.r-project.org},
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394 }</citation>
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395 </citations>
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396 </tool>