Mercurial > repos > artbio > small_rna_maps

annotate small_rna_maps.xml @ 12:d33263e6e812 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
author artbio
date Sat, 07 Apr 2018 06:14:50 -0400
parents a561a71bd7d7
children 458a88317c22
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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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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.5.0">
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>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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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
0
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11 </requirements>
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12 <stdio>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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13 <exit_code range="1:" level="fatal" description="Tool exception" />
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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14 </stdio>
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15 <command detect_errors="exit_code"><![CDATA[
12
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16 #if $inputs_cond.normalize == "no":
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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17 #for $file in $inputs_cond.inputs
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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18 samtools index '$file';
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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19 #end for
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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20 python '$__tool_directory__'/small_rna_maps.py
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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21 --inputs
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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22 #for $file in $inputs_cond.inputs
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23 '$file'
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24 #end for
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25 --sample_names
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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26 #for $sample in $inputs_cond.inputs
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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27 '$sample.name'
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28 #end for
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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29 #else if $inputs_cond.normalize == "yes":
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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30 #for $file in $inputs_cond.series
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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31 samtools index '$file.inputs';
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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32 #end for
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33 python '$__tool_directory__'/small_rna_maps.py
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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34 --inputs
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35 #for $file in $inputs_cond.series
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36 '$file.inputs'
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37 #end for
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38 --sample_names
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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39 #for $sample in $inputs_cond.series
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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40 '$sample.inputs.name'
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41 #end for
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42 #end if
8
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43 --minsize $minsize
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44 --maxsize $maxsize
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45 --cluster $cluster
5
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46 #if str($plots_options.plots_options_selector ) == "two_plot":
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47 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
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48 --outputs '$output_tab' '$extra_output_tab';
7
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49 #elif str($plots_options.plots_options_selector ) == "global":
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50 --plot_methods 'Size'
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51 --outputs '$output_tab';
5
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52 #else:
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53 --plot_methods '${plots_options.first_plot}'
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54 --outputs '$output_tab' ;
5
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55 #end if
2
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56 Rscript '$__tool_directory__'/small_rna_maps.r
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57 --first_dataframe '$output_tab'
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58 --extra_dataframe '$extra_output_tab'
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59 --normalization
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60 #if $inputs_cond.normalize == "no":
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61 ''
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62 #else if $inputs_cond.normalize == "yes":
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63 #set $norm = ""
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64 #for $file in $inputs_cond.series
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65 #set $norm += str($file.normalization)+' '
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66 #end for
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67 #set $norm = $norm[:-1]
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68 '$norm'
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69 #end if
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70 #if $ylimits_cond.ylimits == "no":
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71 --ymin '' --ymax ''
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72 #else:
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73 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
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74 #end if
5
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75 #if str($plots_options.plots_options_selector ) == "two_plot":
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76 --first_plot_method '${plots_options.first_plot}'
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77 --extra_plot_method '${plots_options.extra_plot}'
7
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78 #elif str($plots_options.plots_options_selector ) == "global":
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79 --first_plot_method 'Size'
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80 --extra_plot_method ''
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81 --global '${plots_options.mergestrands}'
5
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82 #else:
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83 --first_plot_method '${plots_options.first_plot}'
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84 --extra_plot_method ''
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85 #end if
7
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86 --output_pdf '$output_pdf'
0
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diff changeset
87 ]]></command>
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88 <inputs>
12
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89 <conditional name="inputs_cond">
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90 <param name="normalize" type="boolean" label="Will there be normalization?" truevalue="yes" falsevalue="no" checked="false"/>
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91 <when value="no">
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92 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
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93 </when>
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94 <when value="yes">
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artbio
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95 <repeat name="series" title="Normalization factors" min="1">
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artbio
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96 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" />
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97 <param name="normalization" type="float" label="Enter size/normalization factors."
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98 help="e.g. '0.75' '1.23'" value="1.0"/>
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99 </repeat>
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100 </when>
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101 </conditional>
8
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102 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
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103 value="0" help="default value: 0" />
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104 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
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105 value="10000" help="default value: 10000" />
12
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106 <param name="cluster" type="integer" label="Aggregation distance in nucleotides"
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107 value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" />
5
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108 <conditional name="plots_options">
7
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109 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
5
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110 <option value="one_plot">Just one plot per chromosome</option>
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111 <option value="two_plot" selected="True">Two plots per chromosome</option>
7
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112 <option value="global">Global read size distributions of aligned reads</option>
5
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113 </param>
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114 <when value="two_plot">
12
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115 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
5
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116 <option value="Counts">Counts</option>
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117 <option value="Coverage">Coverage</option>
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118 <option value="Mean">Mean Sizes</option>
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artbio
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119 <option value="Median">Median Sizes</option>
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120 <option value="Size">Size Distributions</option>
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121 </param>
12
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122 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
5
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123 <option value="Counts">Counts</option>
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124 <option value="Coverage">Coverage</option>
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artbio
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125 <option value="Mean">Mean Sizes</option>
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artbio
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126 <option value="Median">Median Sizes</option>
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127 <option value="Size">Size Distributions</option>
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128 </param>
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129 </when>
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130 <when value="one_plot">
12
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131 <param name="first_plot" type="select" display="radio" label="select the type of plot">
5
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132 <option value="Counts">Counts</option>
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133 <option value="Coverage">Coverage</option>
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134 <option value="Mean">Mean Sizes</option>
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135 <option value="Median">Median Sizes</option>
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136 <option value="Size">Size Distributions</option>
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137 </param>
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138 </when>
7
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139 <when value="global">
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140 <param name="first_plot" type="hidden" value="Size"/>
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141 <param name="mergestrands" type="select" display="radio" label="Whether forward and reverse aligned reads should be merged or not in the histogram">
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142 <option value="nomerge">Do not merge</option>
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143 <option value="merge">Merge forward and reverse reads</option>
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144 </param>
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145 </when>
5
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146 </conditional>
12
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147 <conditional name="ylimits_cond">
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148 <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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149 help="This limit won't be applied to size distribution plots"/>
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150 <when value="yes">
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151 <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/>
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152 <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/>
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153 </when>
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154 <when value="no">
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155 </when>
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156 </conditional>
0
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157 </inputs>
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158
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159 <outputs>
7
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160 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
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161 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
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162 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
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163 </data>
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164 <data format="pdf" name="output_pdf" label="small RNA maps" />
0
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165 </outputs>
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166
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167 <tests>
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168 <test>
12
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169 <param name="inputs" value="input1.bam" ftype="bam"/>
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170 <param name="minsize" value="0" />
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artbio
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171 <param name="maxsize" value="10000" />
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artbio
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172 <param name="cluster" 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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173 <param name="ylimits" value="yes" />
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artbio
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174 <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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175 <param name="ymax" value="5" />
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artbio
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176 <param name="plots_options_selector" value="one_plot" />
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artbio
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177 <param name="first_plot" value="Counts" />
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artbio
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178 <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
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artbio
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179 <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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180 </test>
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181 <test>
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artbio
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182 <param name="inputs" value="input1.bam" ftype="bam"/>
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artbio
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183 <param name="minsize" value="0" />
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artbio
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184 <param name="maxsize" value="10000" />
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artbio
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185 <param name="cluster" 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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186 <param name="plots_options_selector" value="one_plot" />
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artbio
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187 <param name="first_plot" value="Coverage" />
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artbio
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188 <output file="input1_coverage_cluster5.tab" name="output_tab" />
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artbio
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189 <output file="input1_cluster5_single_plot_coverage.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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190 </test>
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191 <test>
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artbio
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192 <param name="inputs" value="input1.bam" ftype="bam"/>
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artbio
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193 <param name="minsize" value="20" />
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artbio
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194 <param name="maxsize" value="30" />
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artbio
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195 <param name="cluster" value="0" />
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artbio
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196 <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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197 <param name="first_plot" value="Size" />
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198 <output file="input1_min20_max30_size.tab" name="output_tab" />
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artbio
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199 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
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200 </test>
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201 <test>
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artbio
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202 <param name="inputs" value="input1.bam" ftype="bam"/>
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artbio
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203 <param name="minsize" value="0" />
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artbio
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204 <param name="maxsize" value="10000" />
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artbio
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205 <param name="cluster" value="0" />
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artbio
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206 <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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207 <param name="first_plot" value="Mean" />
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artbio
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208 <output file="input1_mean.tab" name="output_tab" />
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artbio
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209 <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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210 </test>
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artbio
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211 <test>
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artbio
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212 <param name="inputs" value="input1.bam" ftype="bam"/>
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artbio
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213 <param name="minsize" value="0" />
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artbio
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214 <param name="maxsize" value="10000" />
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artbio
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215 <param name="cluster" value="0" />
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artbio
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216 <param name="plots_options_selector" value="one_plot" />
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artbio
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217 <param name="first_plot" value="Median" />
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218 <output file="input1_median.tab" name="output_tab" />
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219 <output file="input1_single_plot_median.pdf" name="output_pdf" />
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220 </test>
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221 <test>
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artbio
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222 <param name="normalize" value="yes" />
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artbio
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223 <repeat name="series">
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artbio
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224 <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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225 <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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226 </repeat>
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artbio
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227 <repeat name="series">
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artbio
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228 <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
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229 <param name="normalization" value="2.0" />
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230 </repeat>
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artbio
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231 <param name="minsize" value="0" />
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artbio
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232 <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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233 <param name="cluster" 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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234 <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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235 <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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236 <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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237 <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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238 </test>
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239 <test>
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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240 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
8
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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241 <param name="minsize" value="0" />
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artbio
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242 <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
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243 <param name="cluster" 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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244 <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
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245 <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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246 <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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247 <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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248 <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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249 <param name="extra_plot" value="Size" />
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artbio
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250 <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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251 <output file="input1_input2_size.tab" name="extra_output_tab" />
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252 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
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253 </test>
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254 <test>
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255 <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam"/>
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256 <param name="minsize" value="0" />
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257 <param name="maxsize" value="10000" />
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258 <param name="cluster" value="0" />
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259 <param name="plots_options_selector" value="one_plot" />
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260 <param name="first_plot" value="Coverage" />
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261 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
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262 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
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263 </test>
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264 <test>
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265 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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266 <param name="minsize" value="0" />
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267 <param name="maxsize" value="10000" />
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268 <param name="cluster" value="0" />
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269 <param name="plots_options_selector" value="global" />
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270 <param name="mergestrands" value="nomerge" />
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271 <param name="first_plot" value="Size" />
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272 <param name="normalization" value="1 1" />
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273 <output file="size.tab" name="output_tab" />
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274 <output file="global_nomerge.pdf" name="output_pdf" />
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275 </test>
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276 <test>
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277 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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278 <param name="minsize" value="0" />
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279 <param name="maxsize" value="10000" />
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280 <param name="cluster" value="0" />
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281 <param name="plots_options_selector" value="global" />
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282 <param name="mergestrands" value="merge" />
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283 <param name="first_plot" value="Size" />
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284 <param name="normalization" value="1 1" />
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285 <output file="size.tab" name="output_tab" />
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286 <output file="global_merge.pdf" name="output_pdf" />
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287 </test>
0
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288 </tests>
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289 <help>
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290
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291 **What it does**
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292
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293 Plots mapping statistics of an alignment along the reference chromosomes :
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294
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295 - counts
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296 - mean sizes
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297 - median sizes
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298 - coverage depth
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299 - size distribution
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300
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301 Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads
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302 in each position of a chromosome reference.
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303 Coverage depths are computed from the input bam alignment files using the python pysam module.
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304
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305 The metrics mentioned above can be plotted either separately:
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306
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307 .. image:: one_plot.png
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308
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309 Or in all possible pairwise combinations:
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310
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311 .. image:: two_plot.png
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312
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313 For comparison purposes, values from bam alignment files can be normalized by a size factor
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314 before plotting.
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315
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316 **Inputs**
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317
2
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318 bam alignment files that must be
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319
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320 - single-read
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321 - sorted
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322 - mapped to the same reference
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323
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324 **Output**
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325
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326 A pdf file generated by the R package lattice and one or two dataframes used to plot the data.
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327
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328 </help>
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329
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330 <citations>
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331 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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332 <citation type="bibtex">@Book{,
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333 title = {Lattice: Multivariate Data Visualization with R},
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334 author = {Deepayan Sarkar},
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335 publisher = {Springer},
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336 address = {New York},
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337 year = {2008},
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338 note = {ISBN 978-0-387-75968-5},
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339 url = {http://lmdvr.r-forge.r-project.org},
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340 }</citation>
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341 </citations>
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342 </tool>
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343