Mercurial > repos > artbio > small_rna_maps

annotate small_rna_maps.xml @ 18:2c95c899d0a4 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
author artbio
date Thu, 22 Nov 2018 03:07:41 -0500
parents b28dcd4051e8
children f33afecac67a
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18
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.9.0">
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 ${plots_options.cluster}
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41 --bed '$output_bed'
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42 --bed_skipcluster ${plots_options.skip_cluster}
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43 ${plots_options.strandness} &&
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44 #else:
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45 --plot_methods '${plots_options.first_plot}'
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46 --outputs '$output_tab' &&
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47 #end if
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48
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49
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50 Rscript '$__tool_directory__'/small_rna_maps.r
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51 --first_dataframe '$output_tab'
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52 --extra_dataframe '$extra_output_tab'
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53 --normalization
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54 #set $norm = ""
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55 #for $file in $series
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56 #set $norm += str($file.normalization)+' '
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57 #end for
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58 #set $norm = $norm[:-1]
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59 '$norm'
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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 '${plots_options.first_plot}'
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74 --extra_plot_method ''
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75 #end if
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76 --output_pdf '$output_pdf'
0
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77 ]]></command>
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78 <inputs>
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79 <repeat name="series" title="Input" min="1">
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80 <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false"
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81 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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82 <param name="normalization" type="float" label="Enter a size/normalization factor."
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parents: 12
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83 help="Enter only one value e.g. '0.75' or '1.23'" value="1.0"/>
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84 </repeat>
8
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85 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
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86 value="0" help="default value: 0" />
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87 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
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88 value="10000" help="default value: 10000" />
5
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parents: 4
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89 <conditional name="plots_options">
7
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artbio
parents: 6
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90 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
5
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91 <option value="one_plot">Just one plot per chromosome</option>
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92 <option value="two_plot" selected="True">Two plots per chromosome</option>
15
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93 <option value="global">Global read size distributions of aligned reads</option>
16
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94 <option value="cluster">Map read clusters</option>
5
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parents: 4
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95 </param>
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96 <when value="two_plot">
12
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97 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
15
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98 <option value="Counts">Counts</option>
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99 <option value="Coverage">Coverage</option>
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artbio
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100 <option value="Mean">Mean Sizes</option>
5
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artbio
parents: 4
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101 <option value="Median">Median Sizes</option>
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artbio
parents: 4
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102 <option value="Size">Size Distributions</option>
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103 </param>
12
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104 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
15
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105 <option value="Counts">Counts</option>
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artbio
parents: 14
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106 <option value="Coverage">Coverage</option>
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parents: 14
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107 <option value="Mean">Mean Sizes</option>
5
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artbio
parents: 4
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108 <option value="Median">Median Sizes</option>
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artbio
parents: 4
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109 <option value="Size">Size Distributions</option>
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110 </param>
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parents: 4
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111 </when>
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112 <when value="one_plot">
12
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113 <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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114 <option value="Counts">Counts</option>
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parents: 14
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115 <option value="Coverage">Coverage</option>
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artbio
parents: 14
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116 <option value="Mean">Mean Sizes</option>
5
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artbio
parents: 4
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117 <option value="Median">Median Sizes</option>
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artbio
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118 <option value="Size">Size Distributions</option>
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119 </param>
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120 </when>
7
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artbio
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121 <when value="global">
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122 <param name="first_plot" type="hidden" value="Size"/>
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artbio
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123 <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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124 <option value="nomerge">Do not merge</option>
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artbio
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125 <option value="merge">Merge forward and reverse reads</option>
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126 </param>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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127 </when>
16
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128 <when value="cluster">
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129 <param name="first_plot" type="hidden" value="Counts"/>
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130 <param name="cluster" type="integer" label="Aggregation distance in nucleotides" value="1"
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131 help="Sets the distance (in nt) below which reads are clustered to a single median position" />
17
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132 <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false"
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133 label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/>
18
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134 <param name="skip_cluster" type="integer" label="do not report cluster equal or less than the specified number of nucleotides" value="0"
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135 help="Set the number of nucleotides in the cluster for which and below which a cluster is not reported in the bed output. Set to 0 (default) reports all including singlets" />
16
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136 </when>
5
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137 </conditional>
12
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138 <conditional name="ylimits_cond">
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139 <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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140 help="This limit won't be applied to size distribution plots"/>
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141 <when value="yes">
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142 <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/>
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143 <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/>
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144 </when>
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145 <when value="no">
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146 </when>
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147 </conditional>
0
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148 </inputs>
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149
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150 <outputs>
7
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151 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
18
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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152 <data format="bed" name="output_bed" label="bed file for clusters" >
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153 <filter>plots_options['plots_options_selector'] == 'cluster'</filter>
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154 </data>
7
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155 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
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156 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
15
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157 </data>
7
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158 <data format="pdf" name="output_pdf" label="small RNA maps" />
0
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159 </outputs>
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160
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diff changeset
161 <tests>
17
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diff changeset
162 <test> <!-- 0 -->
13
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diff changeset
163 <repeat name="series">
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diff changeset
164 <param name="inputs" value="input1.bam" ftype="bam" />
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165 <param name="normalization" value="1.0" />
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166 </repeat>
15
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167 <repeat name="series">
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168 <param name="inputs" value="input_new2.bam" ftype="bam" />
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169 <param name="normalization" value="2.0" />
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170 </repeat>
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171 <param name="minsize" value="0" />
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172 <param name="maxsize" value="10000" />
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173 <param name="plots_options_selector" value="one_plot" />
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174 <param name="first_plot" value="Counts" />
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175 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
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176 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
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177 </test>
17
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178 <test> <!-- 1 -->
15
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179 <repeat name="series">
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180 <param name="inputs" value="input1.bam" ftype="bam" />
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181 <param name="normalization" value="1.0" />
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182 </repeat>
12
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183 <param name="minsize" value="0" />
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184 <param name="maxsize" value="10000" />
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185 <param name="ylimits" value="yes" />
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186 <param name="ymin" value="-5" />
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187 <param name="ymax" value="5" />
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188 <param name="plots_options_selector" value="one_plot" />
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artbio
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189 <param name="first_plot" value="Counts" />
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190 <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
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191 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
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192 </test>
17
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193 <test> <!-- 2 -->
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194 <repeat name="series">
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195 <param name="inputs" value="input1.bam" ftype="bam" />
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196 <param name="normalization" value="1.0" />
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197 </repeat>
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198 <param name="minsize" value="0" />
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199 <param name="maxsize" value="10000" />
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200 <param name="plots_options_selector" value="cluster" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
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201 <param name="first_plot" value="Counts" />
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202 <param name="cluster" value="5" />
18
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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203 <param name="skip_cluster" value="0" />
17
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204 <param name="strandness" value="false" />
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205 <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
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206 <output file="clustering.pdf" name="output_pdf" />
18
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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207 <output file="bed1.bed" name="output_bed" />
17
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208 </test>
16
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209 <test> <!-- 3 -->
13
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diff changeset
210 <repeat name="series">
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artbio
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diff changeset
211 <param name="inputs" value="input1.bam" ftype="bam" />
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artbio
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212 <param name="normalization" value="1.0" />
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213 </repeat>
12
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artbio
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214 <param name="minsize" value="0" />
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215 <param name="maxsize" value="10000" />
16
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216 <param name="plots_options_selector" value="cluster" />
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217 <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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218 <param name="cluster" value="5" />
18
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219 <param name="skip_cluster" value="0" />
17
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220 <param name="strandness" value="true" />
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221 <output file="clustering_unstranded.tab" name="output_tab" />
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222 <output file="clustering_unstranded.pdf" name="output_pdf" />
18
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223 <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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224 </test>
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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225 <test> <!-- 3.1 -->
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226 <repeat name="series">
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artbio
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227 <param name="inputs" value="input1.bam" ftype="bam" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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228 <param name="normalization" value="1.0" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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229 </repeat>
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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230 <param name="minsize" value="0" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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231 <param name="maxsize" value="10000" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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232 <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
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233 <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
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234 <param name="cluster" value="5" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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235 <param name="skip_cluster" value="1" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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236 <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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237 <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
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238 <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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239 <output file="bed3.bed" name="output_bed" />
12
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240 </test>
16
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241 <test> <!-- 4 -->
13
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diff changeset
242 <repeat name="series">
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artbio
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diff changeset
243 <param name="inputs" value="input1.bam" ftype="bam" />
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244 <param name="normalization" value="1.0" />
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245 </repeat>
12
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246 <param name="minsize" value="20" />
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artbio
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247 <param name="maxsize" value="30" />
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248 <param name="plots_options_selector" value="one_plot" />
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249 <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
parents: 11
diff changeset
250 <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
parents: 11
diff changeset
251 <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
artbio
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diff changeset
252 </test>
16
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artbio
parents: 15
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253 <test> <!-- 5 -->
13
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
254 <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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diff changeset
255 <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
parents: 12
diff changeset
256 <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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257 </repeat>
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
258 <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
parents: 11
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259 <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
parents: 11
diff changeset
260 <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
parents: 11
diff changeset
261 <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
parents: 11
diff changeset
262 <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
parents: 11
diff changeset
263 <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
artbio
parents: 11
diff changeset
264 </test>
16
600e2498bd21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
artbio
parents: 15
diff changeset
265 <test> <!-- 6 -->
13
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
266 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
267 <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
268 <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
parents: 12
diff changeset
269 </repeat>
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
270 <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
parents: 11
diff changeset
271 <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
parents: 11
diff changeset
272 <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
273 <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
artbio
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diff changeset
274 <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
artbio
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diff changeset
275 <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
artbio
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diff changeset
276 </test>
16
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artbio
parents: 15
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277 <test> <!-- 7 -->
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
278 <repeat name="series">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
279 <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
parents: 11
diff changeset
280 <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
parents: 11
diff changeset
281 </repeat>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
282 <repeat name="series">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
283 <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
artbio
parents: 11
diff changeset
284 <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
parents: 11
diff changeset
285 </repeat>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
286 <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
parents: 11
diff changeset
287 <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
parents: 11
diff changeset
288 <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
parents: 11
diff changeset
289 <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
parents: 11
diff changeset
290 <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
parents: 11
diff changeset
291 <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
artbio
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diff changeset
292 </test>
16
600e2498bd21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
artbio
parents: 15
diff changeset
293 <test> <!-- 8 -->
13
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
294 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
295 <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
parents: 12
diff changeset
296 <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
parents: 12
diff changeset
297 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
298 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
299 <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
parents: 12
diff changeset
300 <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
301 </repeat>
8
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents: 7
diff changeset
302 <param name="minsize" value="0" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents: 7
diff changeset
303 <param name="maxsize" value="10000" />
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
304 <param name="ylimits" value="yes" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
305 <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
parents: 11
diff changeset
306 <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
parents: 11
diff changeset
307 <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
parents: 11
diff changeset
308 <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
parents: 11
diff changeset
309 <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
parents: 11
diff changeset
310 <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
parents: 11
diff changeset
311 <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
parents: 11
diff changeset
312 <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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diff changeset
313 </test>
16
600e2498bd21 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 82bb0971cde6ba1972588c9315c3007bc3a5a6a7-dirty
artbio
parents: 15
diff changeset
314 <test> <!-- 9 -->
13
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
315 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
316 <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
parents: 12
diff changeset
317 <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
parents: 12
diff changeset
318 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
319 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
320 <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
parents: 12
diff changeset
321 <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
parents: 12
diff changeset
322 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
323 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
324 <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
parents: 12
diff changeset
325 <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
parents: 12
diff changeset
326 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
327 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
328 <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
parents: 12
diff changeset
329 <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
parents: 12
diff changeset
330 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
331 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
parents: 12
diff changeset
332 <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
parents: 12
diff changeset
333 <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
parents: 12
diff changeset
334 </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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335 <repeat name="series">
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336 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
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337 <param name="normalization" value="1.0" />
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338 </repeat>
12
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339 <param name="minsize" value="0" />
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340 <param name="maxsize" value="10000" />
9
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341 <param name="plots_options_selector" value="one_plot" />
12
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342 <param name="first_plot" value="Coverage" />
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artbio
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343 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
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344 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
9
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345 </test>
16
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346 <test> <!-- 10 -->
13
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347 <repeat name="series">
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artbio
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348 <param name="inputs" value="input1.bam" ftype="bam" />
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artbio
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349 <param name="normalization" value="1.0" />
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350 </repeat>
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artbio
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351 <repeat name="series">
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artbio
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352 <param name="inputs" value="input2.bam" ftype="bam" />
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artbio
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353 <param name="normalization" value="1.0" />
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354 </repeat>
9
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355 <param name="minsize" value="0" />
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356 <param name="maxsize" value="10000" />
7
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artbio
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357 <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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358 <param name="mergestrands" value="nomerge" />
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359 <param name="first_plot" value="Size" />
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artbio
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360 <output file="size.tab" name="output_tab" />
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361 <output file="global_nomerge.pdf" name="output_pdf" />
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362 </test>
16
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363 <test> <!-- 11 -->
13
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364 <repeat name="series">
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365 <param name="inputs" value="input1.bam" ftype="bam" />
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artbio
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366 <param name="normalization" value="1.0" />
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367 </repeat>
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artbio
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368 <repeat name="series">
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369 <param name="inputs" value="input2.bam" ftype="bam" />
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artbio
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370 <param name="normalization" value="1.0" />
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371 </repeat>
8
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artbio
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372 <param name="minsize" value="0" />
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373 <param name="maxsize" value="10000" />
7
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artbio
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374 <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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375 <param name="mergestrands" value="merge" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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376 <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
artbio
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377 <output file="size.tab" name="output_tab" />
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artbio
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378 <output file="global_merge.pdf" name="output_pdf" />
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379 </test>
0
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380 </tests>
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381 <help>
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382
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383 **What it does**
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384
12
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385 Plots mapping statistics of an alignment along the reference chromosomes :
6
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artbio
parents: 5
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386
12
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artbio
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387 - 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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388 - mean sizes
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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389 - median sizes
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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390 - coverage depth
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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391 - size distribution
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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392
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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393 Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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394 in each position of a chromosome reference.
6
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395 Coverage depths are computed from the input bam alignment files using the python pysam module.
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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396
12
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397 The metrics mentioned above can be plotted either separately:
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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398
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399 .. image:: one_plot.png
6
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400
12
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
401 Or in all possible pairwise combinations:
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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402
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artbio
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403 .. image:: two_plot.png
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
404
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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405 For comparison purposes, values from bam alignment files can be normalized by a size factor
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
406 before plotting.
0
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diff changeset
407
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
408 **Inputs**
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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409
2
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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diff changeset
410 bam alignment files that must be
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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diff changeset
411
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
412 - single-read
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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diff changeset
413 - sorted
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
414 - mapped to the same reference
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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415
13
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artbio
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diff changeset
416 To plot 2 alignment files in the same PDF output the 'single dataset' method should be used.
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
417
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artbio
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diff changeset
418 .. class:: warningmark
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
419
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artbio
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diff changeset
420 If the 'multiple dataset' method is used the normalization factor will be applied to every file selected in the input list.
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
421 Additionally each file in the selected list will be plotted in a separate PDF file.
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
422
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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diff changeset
423 **Output**
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424
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425 A pdf file generated by the R package lattice and one or two dataframes used to plot the data.
0
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426
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427 </help>
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428
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429 <citations>
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430 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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431 <citation type="bibtex">@Book{,
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432 title = {Lattice: Multivariate Data Visualization with R},
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433 author = {Deepayan Sarkar},
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434 publisher = {Springer},
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435 address = {New York},
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436 year = {2008},
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437 note = {ISBN 978-0-387-75968-5},
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438 url = {http://lmdvr.r-forge.r-project.org},
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439 }</citation>
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440 </citations>
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441 </tool>