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annotate small_rna_maps.xml @ 16:600e2498bd21 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
author artbio
date Tue, 13 Nov 2018 17:03:46 -0500
parents 82fedc576024
children b28dcd4051e8
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16
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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.7.0">
0
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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>
7
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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[
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16 #for $file in $series
16
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17 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file.inputs' >'$file.inputs.name' &&
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18 samtools index '$file.inputs.name' &&
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19 #end for
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20 python '$__tool_directory__'/small_rna_maps.py
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21 --inputs
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22 #for $file in $series
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23 '$file.inputs.name'
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24 #end for
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25 --sample_names
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26 #for $sample in $series
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27 '$sample.inputs.name'
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28 #end for
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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 ${plots_options.cluster} &&
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41 #else:
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42 --plot_methods '${plots_options.first_plot}'
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43 --outputs '$output_tab' &&
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44 #end if
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45
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46 Rscript '$__tool_directory__'/small_rna_maps.r
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47 --first_dataframe '$output_tab'
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48 --extra_dataframe '$extra_output_tab'
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49 --normalization
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50 #set $norm = ""
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51 #for $file in $series
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52 #set $norm += str($file.normalization)+' '
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53 #end for
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54 #set $norm = $norm[:-1]
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55 '$norm'
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56 #if $ylimits_cond.ylimits == "no":
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57 --ymin '' --ymax ''
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58 #else:
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59 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
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60 #end if
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61 #if str($plots_options.plots_options_selector ) == "two_plot":
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62 --first_plot_method '${plots_options.first_plot}'
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63 --extra_plot_method '${plots_options.extra_plot}'
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64 #elif str($plots_options.plots_options_selector ) == "global":
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65 --first_plot_method 'Size'
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66 --extra_plot_method ''
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67 --global '${plots_options.mergestrands}'
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68 #else:
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69 --first_plot_method '${plots_options.first_plot}'
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70 --extra_plot_method ''
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71 #end if
7
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72 --output_pdf '$output_pdf'
0
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73 ]]></command>
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74 <inputs>
13
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75 <repeat name="series" title="Input" min="1">
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76 <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false"
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77 help="If 'multiple datasets' method is used, the same normalization factor will be applied to each dataset. Please refer to the help section for more information." />
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78 <param name="normalization" type="float" label="Enter a size/normalization factor."
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79 help="Enter only one value e.g. '0.75' or '1.23'" value="1.0"/>
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80 </repeat>
8
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81 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
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82 value="0" help="default value: 0" />
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83 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
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84 value="10000" help="default value: 10000" />
5
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artbio
parents: 4
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85 <conditional name="plots_options">
7
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artbio
parents: 6
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86 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
5
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artbio
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87 <option value="one_plot">Just one plot per chromosome</option>
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artbio
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88 <option value="two_plot" selected="True">Two plots per chromosome</option>
15
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artbio
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89 <option value="global">Global read size distributions of aligned reads</option>
16
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artbio
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90 <option value="cluster">Map read clusters</option>
5
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91 </param>
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artbio
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92 <when value="two_plot">
12
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artbio
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93 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
15
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94 <option value="Counts">Counts</option>
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artbio
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95 <option value="Coverage">Coverage</option>
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artbio
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96 <option value="Mean">Mean Sizes</option>
5
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artbio
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97 <option value="Median">Median Sizes</option>
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artbio
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98 <option value="Size">Size Distributions</option>
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artbio
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99 </param>
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artbio
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100 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
15
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artbio
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101 <option value="Counts">Counts</option>
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102 <option value="Coverage">Coverage</option>
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artbio
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103 <option value="Mean">Mean Sizes</option>
5
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artbio
parents: 4
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104 <option value="Median">Median Sizes</option>
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artbio
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105 <option value="Size">Size Distributions</option>
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106 </param>
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107 </when>
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108 <when value="one_plot">
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artbio
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109 <param name="first_plot" type="select" display="radio" label="select the type of plot">
15
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artbio
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110 <option value="Counts">Counts</option>
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artbio
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111 <option value="Coverage">Coverage</option>
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artbio
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112 <option value="Mean">Mean Sizes</option>
5
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artbio
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113 <option value="Median">Median Sizes</option>
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114 <option value="Size">Size Distributions</option>
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115 </param>
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116 </when>
7
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117 <when value="global">
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118 <param name="first_plot" type="hidden" value="Size"/>
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119 <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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120 <option value="nomerge">Do not merge</option>
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artbio
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121 <option value="merge">Merge forward and reverse reads</option>
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122 </param>
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123 </when>
16
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124 <when value="cluster">
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artbio
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125 <param name="first_plot" type="hidden" value="Counts"/>
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artbio
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126 <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1"
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127 help="Sets the distance (in nt) below which reads are clustered to a single median position" />
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128 </when>
5
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129 </conditional>
12
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130 <conditional name="ylimits_cond">
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131 <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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132 help="This limit won't be applied to size distribution plots"/>
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133 <when value="yes">
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134 <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/>
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135 <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/>
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136 </when>
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137 <when value="no">
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138 </when>
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139 </conditional>
0
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140 </inputs>
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141
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142 <outputs>
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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143 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
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144 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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145 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
15
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146 </data>
7
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147 <data format="pdf" name="output_pdf" label="small RNA maps" />
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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148 </outputs>
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149
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150 <tests>
16
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151 <test> <!-- 1 -->
13
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diff changeset
152 <repeat name="series">
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153 <param name="inputs" value="input1.bam" ftype="bam" />
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154 <param name="normalization" value="1.0" />
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155 </repeat>
15
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diff changeset
156 <repeat name="series">
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157 <param name="inputs" value="input_new2.bam" ftype="bam" />
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158 <param name="normalization" value="2.0" />
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159 </repeat>
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artbio
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diff changeset
160 <param name="minsize" value="0" />
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artbio
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diff changeset
161 <param name="maxsize" value="10000" />
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diff changeset
162 <param name="plots_options_selector" value="one_plot" />
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artbio
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diff changeset
163 <param name="first_plot" value="Counts" />
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164 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
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165 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
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166 </test>
16
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artbio
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167 <test> <!-- 2 -->
15
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artbio
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168 <repeat name="series">
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artbio
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169 <param name="inputs" value="input1.bam" ftype="bam" />
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170 <param name="normalization" value="1.0" />
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artbio
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171 </repeat>
12
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172 <param name="minsize" value="0" />
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artbio
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173 <param name="maxsize" value="10000" />
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174 <param name="ylimits" value="yes" />
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artbio
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175 <param name="ymin" value="-5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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176 <param name="ymax" value="5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
177 <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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178 <param name="first_plot" value="Counts" />
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artbio
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179 <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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180 <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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181 </test>
16
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artbio
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182 <test> <!-- 3 -->
13
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183 <repeat name="series">
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artbio
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184 <param name="inputs" value="input1.bam" ftype="bam" />
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185 <param name="normalization" value="1.0" />
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186 </repeat>
12
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artbio
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187 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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188 <param name="maxsize" value="10000" />
16
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artbio
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189 <param name="plots_options_selector" value="cluster" />
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artbio
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190 <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
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191 <param name="cluster" value="5" />
16
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artbio
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192 <output file="clustering.tab" name="output_tab" />
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193 <output file="clustering.pdf" name="output_pdf" />
12
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194 </test>
16
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artbio
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195 <test> <!-- 4 -->
13
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196 <repeat name="series">
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artbio
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197 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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198 <param name="normalization" value="1.0" />
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artbio
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199 </repeat>
12
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artbio
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200 <param name="minsize" value="20" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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201 <param name="maxsize" value="30" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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202 <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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203 <param name="first_plot" value="Size" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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204 <output file="input1_min20_max30_size.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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205 <output file="input1_min20_max30_single_plot_size.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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diff changeset
206 </test>
16
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artbio
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207 <test> <!-- 5 -->
13
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208 <repeat name="series">
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artbio
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diff changeset
209 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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210 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
211 </repeat>
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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diff changeset
212 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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213 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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214 <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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215 <param name="first_plot" value="Mean" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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216 <output file="input1_mean.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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217 <output file="input1__single_plot_mean.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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218 </test>
16
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219 <test> <!-- 6 -->
13
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220 <repeat name="series">
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artbio
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diff changeset
221 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
222 <param name="normalization" value="1.0" />
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223 </repeat>
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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224 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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225 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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226 <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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227 <param name="first_plot" value="Median" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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228 <output file="input1_median.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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229 <output file="input1_single_plot_median.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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diff changeset
230 </test>
16
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artbio
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231 <test> <!-- 7 -->
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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232 <repeat name="series">
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artbio
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233 <param name="inputs" value="input1.bam" ftype="bam" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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234 <param name="normalization" value="1.0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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235 </repeat>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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236 <repeat name="series">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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237 <param name="inputs" value="input2.bam" ftype="bam" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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238 <param name="normalization" value="2.0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
239 </repeat>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
240 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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241 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
242 <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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diff changeset
243 <param name="first_plot" value="Counts" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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244 <output file="input1_input2_norm_1_2_counts.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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245 <output file="input1_input2_norm_1_2_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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diff changeset
246 </test>
16
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artbio
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247 <test> <!-- 8 -->
13
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diff changeset
248 <repeat name="series">
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artbio
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249 <param name="inputs" value="input1.bam" ftype="bam" />
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artbio
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diff changeset
250 <param name="normalization" value="1.0" />
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251 </repeat>
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artbio
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252 <repeat name="series">
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artbio
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253 <param name="inputs" value="input2.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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254 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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255 </repeat>
8
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artbio
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256 <param name="minsize" value="0" />
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artbio
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257 <param name="maxsize" value="10000" />
12
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artbio
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258 <param name="ylimits" value="yes" />
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artbio
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259 <param name="ymin" value="-5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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260 <param name="ymax" value="5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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261 <param name="plots_options_selector" value="two_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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262 <param name="first_plot" value="Counts" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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263 <param name="extra_plot" value="Size" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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264 <output file="input1_input2_counts.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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265 <output file="input1_input2_size.tab" name="extra_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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266 <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
artbio
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267 </test>
16
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artbio
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268 <test> <!-- 9 -->
13
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artbio
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269 <repeat name="series">
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artbio
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270 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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271 <param name="normalization" value="1.0" />
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artbio
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272 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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273 <repeat name="series">
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artbio
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274 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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275 <param name="normalization" value="1.0" />
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artbio
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276 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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277 <repeat name="series">
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artbio
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diff changeset
278 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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279 <param name="normalization" value="1.0" />
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artbio
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280 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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281 <repeat name="series">
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artbio
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diff changeset
282 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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283 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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284 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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285 <repeat name="series">
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artbio
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286 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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287 <param name="normalization" value="1.0" />
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artbio
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288 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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289 <repeat name="series">
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artbio
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290 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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291 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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292 </repeat>
12
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293 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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294 <param name="maxsize" value="10000" />
9
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
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295 <param name="plots_options_selector" value="one_plot" />
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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296 <param name="first_plot" value="Coverage" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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297 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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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>
16
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artbio
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300 <test> <!-- 10 -->
13
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301 <repeat name="series">
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artbio
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302 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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303 <param name="normalization" value="1.0" />
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artbio
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304 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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305 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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306 <param name="inputs" value="input2.bam" ftype="bam" />
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artbio
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307 <param name="normalization" value="1.0" />
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308 </repeat>
9
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
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309 <param name="minsize" value="0" />
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310 <param name="maxsize" value="10000" />
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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311 <param name="plots_options_selector" value="global" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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312 <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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313 <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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314 <output file="size.tab" name="output_tab" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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315 <output file="global_nomerge.pdf" name="output_pdf" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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316 </test>
16
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317 <test> <!-- 11 -->
13
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318 <repeat name="series">
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319 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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320 <param name="normalization" value="1.0" />
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321 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
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322 <repeat name="series">
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323 <param name="inputs" value="input2.bam" ftype="bam" />
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324 <param name="normalization" value="1.0" />
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325 </repeat>
8
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artbio
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326 <param name="minsize" value="0" />
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327 <param name="maxsize" value="10000" />
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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328 <param name="plots_options_selector" value="global" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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329 <param name="mergestrands" value="merge" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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330 <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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331 <output file="size.tab" name="output_tab" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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332 <output file="global_merge.pdf" name="output_pdf" />
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333 </test>
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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334 </tests>
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335 <help>
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336
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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337 **What it does**
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338
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339 Plots mapping statistics of an alignment along the reference chromosomes :
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340
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341 - counts
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342 - mean sizes
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343 - median sizes
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344 - coverage depth
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345 - size distribution
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346
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347 Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads
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348 in each position of a chromosome reference.
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349 Coverage depths are computed from the input bam alignment files using the python pysam module.
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350
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351 The metrics mentioned above can be plotted either separately:
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352
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353 .. image:: one_plot.png
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354
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355 Or in all possible pairwise combinations:
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356
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357 .. image:: two_plot.png
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358
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359 For comparison purposes, values from bam alignment files can be normalized by a size factor
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360 before plotting.
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361
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362 **Inputs**
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363
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364 bam alignment files that must be
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365
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366 - single-read
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367 - sorted
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368 - mapped to the same reference
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369
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370 To plot 2 alignment files in the same PDF output the 'single dataset' method should be used.
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371
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372 .. class:: warningmark
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373
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374 If the 'multiple dataset' method is used the normalization factor will be applied to every file selected in the input list.
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375 Additionally each file in the selected list will be plotted in a separate PDF file.
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376
0
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377 **Output**
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378
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379 A pdf file generated by the R package lattice and one or two dataframes used to plot the data.
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380
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381 </help>
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382
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383 <citations>
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384 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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385 <citation type="bibtex">@Book{,
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386 title = {Lattice: Multivariate Data Visualization with R},
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387 author = {Deepayan Sarkar},
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388 publisher = {Springer},
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389 address = {New York},
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390 year = {2008},
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391 note = {ISBN 978-0-387-75968-5},
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392 url = {http://lmdvr.r-forge.r-project.org},
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393 }</citation>
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394 </citations>
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395 </tool>