Mercurial > repos > artbio > small_rna_maps

annotate small_rna_maps.xml @ 8:1827b74f872b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
author artbio
date Mon, 23 Oct 2017 08:29:39 -0400
parents a96e6a7df2b7
children 3ea75c573429
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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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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.3.0">
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
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[
2
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16 #for $file in $inputs
0
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17 samtools index '$file' &&
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18 #end for
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19 python '$__tool_directory__'/small_rna_maps.py
2
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20 --inputs
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21 #for $file in $inputs
0
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22 '$file'
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23 #end for
2
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24 --sample_names
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25 #for $sample in $inputs
0
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26 '$sample.name'
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27 #end for
8
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28 --minsize $minsize
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29 --maxsize $maxsize
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30 #if str($plots_options.plots_options_selector ) == "two_plot":
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31 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
3
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32 --outputs '$output_tab' '$extra_output_tab' &&
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33 #elif str($plots_options.plots_options_selector ) == "global":
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34 --plot_methods 'Size'
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35 --outputs '$output_tab' &&
5
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36 #else:
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37 --plot_methods '${plots_options.first_plot}'
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38 --outputs '$output_tab' &&
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39 #end if
2
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40 Rscript '$__tool_directory__'/small_rna_maps.r
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41 --first_dataframe '$output_tab'
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42 --extra_dataframe '$extra_output_tab'
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43 --normalization '$normalization'
5
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44 #if str($plots_options.plots_options_selector ) == "two_plot":
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45 --first_plot_method '${plots_options.first_plot}'
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46 --extra_plot_method '${plots_options.extra_plot}'
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47 #elif str($plots_options.plots_options_selector ) == "global":
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48 --first_plot_method 'Size'
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49 --extra_plot_method ''
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50 --global '${plots_options.mergestrands}'
5
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51 #else:
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52 --first_plot_method '${plots_options.first_plot}'
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53 --extra_plot_method ''
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54 #end if
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55 --output_pdf '$output_pdf'
0
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56 ]]></command>
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57 <inputs>
5
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58 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
6
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59 <param name="normalization" type="text" label="Enter size/normalization factors as a space-separated list. Leave blank for no normalization (default)"
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60 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" />
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61 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
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62 value="0" help="default value: 0" />
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63 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
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64 value="10000" help="default value: 10000" />
5
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65 <conditional name="plots_options">
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66 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
5
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67 <option value="one_plot">Just one plot per chromosome</option>
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68 <option value="two_plot" selected="True">Two plots per chromosome</option>
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69 <option value="global">Global read size distributions of aligned reads</option>
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70 </param>
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71 <when value="two_plot">
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72 <param name="first_plot" type="select" display="radio" label="Select the type of the first plot">
5
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73 <option value="Counts">Counts</option>
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74 <option value="Coverage">Coverage</option>
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75 <option value="Mean">Mean Sizes</option>
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76 <option value="Median">Median Sizes</option>
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77 <option value="Size">Size Distributions</option>
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78 </param>
7
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79 <param name="extra_plot" type="select" display="radio" label="Select the type of the second plot">
5
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80 <option value="Counts">Counts</option>
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81 <option value="Coverage">Coverage</option>
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artbio
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82 <option value="Mean">Mean Sizes</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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83 <option value="Median">Median Sizes</option>
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artbio
parents: 4
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84 <option value="Size">Size Distributions</option>
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85 </param>
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86 </when>
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artbio
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87 <when value="one_plot">
7
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artbio
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88 <param name="first_plot" type="select" display="radio" label="select the type of the first plot">
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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89 <option value="Counts">Counts</option>
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artbio
parents: 4
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90 <option value="Coverage">Coverage</option>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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91 <option value="Mean">Mean Sizes</option>
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artbio
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92 <option value="Median">Median Sizes</option>
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artbio
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93 <option value="Size">Size Distributions</option>
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94 </param>
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95 </when>
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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96 <when value="global">
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artbio
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97 <param name="first_plot" type="hidden" value="Size"/>
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artbio
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98 <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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99 <option value="nomerge">Do not merge</option>
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100 <option value="merge">Merge forward and reverse reads</option>
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101 </param>
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102 </when>
5
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103 </conditional>
0
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104 </inputs>
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105
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106 <outputs>
7
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107 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
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artbio
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108 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
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109 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
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110 </data>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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111 <data format="pdf" name="output_pdf" label="small RNA maps" />
0
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112 </outputs>
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113
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114 <tests>
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115 <test>
2
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artbio
parents: 1
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116 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
8
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117 <param name="minsize" value="0" />
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118 <param name="maxsize" value="10000" />
7
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119 <param name="plots_options_selector" value="global" />
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120 <param name="mergestrands" value="nomerge" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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121 <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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122 <param name="normalization" value="1 1" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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123 <output file="size.tab" name="output_tab" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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124 <output file="global_nomerge.pdf" name="output_pdf" />
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125 </test>
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artbio
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126 <test>
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 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
8
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artbio
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128 <param name="minsize" value="0" />
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artbio
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129 <param name="maxsize" value="10000" />
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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130 <param name="plots_options_selector" value="global" />
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131 <param name="mergestrands" value="merge" />
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132 <param name="first_plot" value="Size" />
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artbio
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133 <param name="normalization" value="1 1" />
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134 <output file="size.tab" name="output_tab" />
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135 <output file="global_merge.pdf" name="output_pdf" />
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136 </test>
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137 <test>
8
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artbio
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diff changeset
138 <param name="inputs" value="input1.bam" ftype="bam"/>
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139 <param name="minsize" value="20" />
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140 <param name="maxsize" value="30" />
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artbio
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diff changeset
141 <param name="plots_options_selector" value="global" />
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artbio
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142 <param name="mergestrands" value="merge" />
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artbio
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143 <param name="first_plot" value="Size" />
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artbio
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144 <param name="normalization" value="1 1" />
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145 <output file="size20-30.tab" name="output_tab" />
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artbio
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146 <output file="global_merge_20-30.pdf" name="output_pdf" />
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147 </test>
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148 <test>
7
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artbio
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149 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
8
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diff changeset
150 <param name="minsize" value="0" />
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151 <param name="maxsize" value="10000" />
5
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diff changeset
152 <param name="plots_options_selector" value="two_plot" />
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artbio
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153 <param name="first_plot" value="Counts" />
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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154 <param name="extra_plot" value="Mean" />
6
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155 <param name="normalization" value="1 1" />
5
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156 <output file="count.tab" name="output_tab" />
2
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artbio
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157 <output file="mean.tab" name="extra_output_tab" />
5
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158 <output file="count-mean.pdf" name="output_pdf" />
0
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159 </test>
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160 <test>
8
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diff changeset
161 <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/>
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artbio
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diff changeset
162 <param name="minsize" value="20" />
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artbio
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diff changeset
163 <param name="maxsize" value="30" />
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artbio
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diff changeset
164 <param name="plots_options_selector" value="two_plot" />
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165 <param name="first_plot" value="Counts" />
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artbio
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166 <param name="extra_plot" value="Mean" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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167 <param name="normalization" value="1 1" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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168 <output file="count20-30.tab" name="output_tab" />
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artbio
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169 <output file="mean20-30.tab" name="extra_output_tab" />
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artbio
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170 <output file="count-mean-20-30.pdf" name="output_pdf" />
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171 </test>
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172 <test>
2
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artbio
parents: 1
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173 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
8
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174 <param name="minsize" value="0" />
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artbio
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175 <param name="maxsize" value="10000" />
5
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artbio
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176 <param name="plots_options_selector" value="two_plot" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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177 <param name="first_plot" value="Counts" />
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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178 <param name="extra_plot" value="Mean" />
6
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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179 <param name="normalization" value="1 1" />
5
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artbio
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180 <output file="doubled_count.tab" name="output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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181 <output file="doubled_mean.tab" name="extra_output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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182 <output file="doubled_count-mean.pdf" name="output_pdf" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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183 </test>
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artbio
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184 <test>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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185 <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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186 <param name="minsize" value="0" />
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artbio
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187 <param name="maxsize" value="10000" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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188 <param name="plots_options_selector" value="two_plot" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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189 <param name="first_plot" value="Counts" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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190 <param name="extra_plot" value="Median" />
6
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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191 <param name="normalization" value="1 1" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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192 <output file="count.tab" name="output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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193 <output file="median.tab" name="extra_output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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194 <output file="count-median.pdf" name="output_pdf" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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195 </test>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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196 <test>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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197 <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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198 <param name="minsize" value="0" />
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artbio
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199 <param name="maxsize" value="10000" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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200 <param name="plots_options_selector" value="two_plot" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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201 <param name="first_plot" value="Counts" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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202 <param name="extra_plot" value="Coverage" />
6
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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203 <param name="normalization" value="1 1" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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204 <output file="count.tab" name="output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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205 <output file="coverage.tab" name="extra_output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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206 <output file="count-coverage.pdf" name="output_pdf" />
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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207 </test>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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208 <test>
2
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artbio
parents: 1
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209 <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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diff changeset
210 <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
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211 <param name="maxsize" value="10000" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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diff changeset
212 <param name="plots_options_selector" value="two_plot" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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213 <param name="first_plot" value="Counts" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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214 <param name="extra_plot" value="Size" />
6
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
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215 <param name="normalization" value="1 1" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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216 <output file="count.tab" name="output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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217 <output file="size.tab" name="extra_output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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218 <output file="count-size.pdf" name="output_pdf" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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219 </test>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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220 <test>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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221 <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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222 <param name="minsize" value="0" />
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223 <param name="maxsize" value="10000" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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224 <param name="plots_options_selector" value="two_plot" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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225 <param name="first_plot" value="Size" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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226 <param name="extra_plot" value="Counts" />
6
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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227 <param name="normalization" value="1 1" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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228 <output file="size.tab" name="output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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229 <output file="count.tab" name="extra_output_tab" />
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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230 <output file="size-count.pdf" name="output_pdf" />
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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231 </test>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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232 <test>
2
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artbio
parents: 1
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233 <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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234 <param name="minsize" value="0" />
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235 <param name="maxsize" value="10000" />
6
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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236 <param name="plots_options_selector" value="two_plot" />
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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diff changeset
237 <param name="first_plot" value="Size" />
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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diff changeset
238 <param name="extra_plot" value="Counts" />
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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diff changeset
239 <param name="normalization" value="1 0.75" />
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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240 <output file="size.tab" name="output_tab" />
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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diff changeset
241 <output file="count.tab" name="extra_output_tab" />
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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diff changeset
242 <output file="size-count_normed.pdf" name="output_pdf" />
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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243 </test>
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
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244 <test>
a3be3601bcb3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 9f9c64aff0d225881bedb97bd5035ccbca945d9d
artbio
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diff changeset
245 <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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246 <param name="minsize" value="0" />
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artbio
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247 <param name="maxsize" value="10000" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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248 <param name="plots_options_selector" value="one_plot" />
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249 <param name="normalization" value="1 1" />
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250 <param name="first_plot" value="Counts" />
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251 <output file="count.tab" name="output_tab" />
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252 <output file="count.pdf" name="output_pdf" />
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253 </test>
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254 <test>
2
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255 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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256 <param name="minsize" value="0" />
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257 <param name="maxsize" value="10000" />
5
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258 <param name="plots_options_selector" value="one_plot" />
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259 <param name="first_plot" value="Size" />
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260 <param name="normalization" value="1 1" />
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261 <output file="size.tab" name="output_tab" />
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262 <output file="size.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="plots_options_selector" value="one_plot" />
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269 <param name="first_plot" value="Coverage" />
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270 <param name="normalization" value="1 1" />
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271 <output file="coverage.tab" name="output_tab" />
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272 <output file="coverage.pdf" name="output_pdf" />
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273 </test>
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274 <test>
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275 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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276 <param name="minsize" value="0" />
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277 <param name="maxsize" value="10000" />
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278 <param name="plots_options_selector" value="one_plot" />
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279 <param name="first_plot" value="Coverage" />
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280 <param name="normalization" value="1 0.2" />
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281 <output file="coverage.tab" name="output_tab" />
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282 <output file="coverage_normed.pdf" name="output_pdf" />
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283 </test>
0
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284 </tests>
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285
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286
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287 <help>
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288
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289 **What it does**
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290
6
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291 Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5)
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292 size read distribution along chromosome references.
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293
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294 Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads
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295 whose 5' end map to a given coordinate in a chromosome reference.
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296 Coverage depths are computed from the input bam alignment files using the python pysam module.
0
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297
6
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298 The variables mentioned above (1-5) can be plotted either separately or in all possible
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299 pairwise combinations.
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300
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301 For comparison purpose, values from bam alignment files can be normalized by a size factor
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302 before plotting. If the normalization field is leaved blank, default normalization of 1
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303 is assumed.
0
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304
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305 **Inputs**
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306
2
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307 bam alignment files that must be
0
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308
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309 - single-read
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310 - sorted
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311 - mapping to the same reference
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312
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313 Optionally, a space-separated list of normalization/size factors may be added before plotting.
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314 This list maps to the selected bam alignments from bottom to top.
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315
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316 **Output**
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317
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318 A pdf file generated by the R package lattice
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319
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320 One or two dataframes used to plot data
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321
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322 </help>
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323
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324 <citations>
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325 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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326 <citation type="bibtex">@Book{,
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327 title = {Lattice: Multivariate Data Visualization with R},
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328 author = {Deepayan Sarkar},
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329 publisher = {Springer},
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330 address = {New York},
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331 year = {2008},
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332 note = {ISBN 978-0-387-75968-5},
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333 url = {http://lmdvr.r-forge.r-project.org},
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334 }</citation>
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335 </citations>
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336 </tool>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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