Mercurial > repos > artbio > small_rna_maps

annotate small_rna_maps.xml @ 7:a96e6a7df2b7 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
author artbio
date Tue, 10 Oct 2017 18:48:37 -0400
parents a3be3601bcb3
children 1827b74f872b
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7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.2.0">
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>
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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
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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
5
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28 #if str($plots_options.plots_options_selector ) == "two_plot":
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29 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
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30 --outputs '$output_tab' '$extra_output_tab' &&
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31 #elif str($plots_options.plots_options_selector ) == "global":
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32 --plot_methods 'Size'
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33 --outputs '$output_tab' &&
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34 #else:
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35 --plot_methods '${plots_options.first_plot}'
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36 --outputs '$output_tab' &&
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37 #end if
2
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38 Rscript '$__tool_directory__'/small_rna_maps.r
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39 --first_dataframe '$output_tab'
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40 --extra_dataframe '$extra_output_tab'
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41 --normalization '$normalization'
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42 #if str($plots_options.plots_options_selector ) == "two_plot":
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43 --first_plot_method '${plots_options.first_plot}'
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44 --extra_plot_method '${plots_options.extra_plot}'
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45 #elif str($plots_options.plots_options_selector ) == "global":
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46 --first_plot_method 'Size'
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47 --extra_plot_method ''
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48 --global '${plots_options.mergestrands}'
5
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49 #else:
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50 --first_plot_method '${plots_options.first_plot}'
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51 --extra_plot_method ''
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52 #end if
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53 --output_pdf '$output_pdf'
0
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54 ]]></command>
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55 <inputs>
5
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56 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
6
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57 <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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58 help="e.g. '1 0.75 1.23'. Values of the list map to the above selected files from bottom to top" />
5
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59 <conditional name="plots_options">
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60 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
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61 <option value="one_plot">Just one plot per chromosome</option>
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62 <option value="two_plot" selected="True">Two plots per chromosome</option>
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63 <option value="global">Global read size distributions of aligned reads</option>
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64 </param>
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65 <when value="two_plot">
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66 <param name="first_plot" type="select" display="radio" label="Select the type of the first plot">
5
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67 <option value="Counts">Counts</option>
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68 <option value="Coverage">Coverage</option>
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69 <option value="Mean">Mean Sizes</option>
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70 <option value="Median">Median Sizes</option>
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71 <option value="Size">Size Distributions</option>
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72 </param>
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73 <param name="extra_plot" type="select" display="radio" label="Select the type of the second plot">
5
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74 <option value="Counts">Counts</option>
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75 <option value="Coverage">Coverage</option>
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76 <option value="Mean">Mean Sizes</option>
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77 <option value="Median">Median Sizes</option>
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78 <option value="Size">Size Distributions</option>
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79 </param>
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80 </when>
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81 <when value="one_plot">
7
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82 <param name="first_plot" type="select" display="radio" label="select the type of the first plot">
5
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83 <option value="Counts">Counts</option>
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84 <option value="Coverage">Coverage</option>
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85 <option value="Mean">Mean Sizes</option>
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artbio
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86 <option value="Median">Median Sizes</option>
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artbio
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87 <option value="Size">Size Distributions</option>
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88 </param>
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89 </when>
7
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90 <when value="global">
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91 <param name="first_plot" type="hidden" value="Size"/>
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artbio
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92 <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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93 <option value="nomerge">Do not merge</option>
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94 <option value="merge">Merge forward and reverse reads</option>
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95 </param>
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96 </when>
5
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97 </conditional>
0
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98 </inputs>
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99
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100 <outputs>
7
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101 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
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102 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
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103 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
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104 </data>
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105 <data format="pdf" name="output_pdf" label="small RNA maps" />
0
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106 </outputs>
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107
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108 <tests>
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109 <test>
2
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110 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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111 <param name="plots_options_selector" value="global" />
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112 <param name="mergestrands" value="nomerge" />
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113 <param name="first_plot" value="Size" />
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114 <param name="normalization" value="1 1" />
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115 <output file="size.tab" name="output_tab" />
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116 <output file="global_nomerge.pdf" name="output_pdf" />
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117 </test>
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artbio
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118 <test>
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artbio
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119 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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120 <param name="plots_options_selector" value="global" />
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121 <param name="mergestrands" value="merge" />
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122 <param name="first_plot" value="Size" />
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artbio
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123 <param name="normalization" value="1 1" />
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124 <output file="size.tab" name="output_tab" />
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125 <output file="global_merge.pdf" name="output_pdf" />
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126 </test>
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127 <test>
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128 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
5
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129 <param name="plots_options_selector" value="two_plot" />
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130 <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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131 <param name="extra_plot" value="Mean" />
6
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132 <param name="normalization" value="1 1" />
5
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133 <output file="count.tab" name="output_tab" />
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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134 <output file="mean.tab" name="extra_output_tab" />
5
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135 <output file="count-mean.pdf" name="output_pdf" />
0
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136 </test>
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137 <test>
2
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138 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
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139 <param name="plots_options_selector" value="two_plot" />
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140 <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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141 <param name="extra_plot" value="Mean" />
6
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142 <param name="normalization" value="1 1" />
5
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143 <output file="doubled_count.tab" name="output_tab" />
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144 <output file="doubled_mean.tab" name="extra_output_tab" />
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145 <output file="doubled_count-mean.pdf" name="output_pdf" />
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146 </test>
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147 <test>
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148 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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149 <param name="plots_options_selector" value="two_plot" />
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150 <param name="first_plot" value="Counts" />
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151 <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
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152 <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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153 <output file="count.tab" name="output_tab" />
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154 <output file="median.tab" name="extra_output_tab" />
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155 <output file="count-median.pdf" name="output_pdf" />
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156 </test>
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157 <test>
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artbio
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diff changeset
158 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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diff changeset
159 <param name="plots_options_selector" value="two_plot" />
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160 <param name="first_plot" value="Counts" />
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artbio
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161 <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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diff changeset
162 <param name="normalization" value="1 1" />
5
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163 <output file="count.tab" name="output_tab" />
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164 <output file="coverage.tab" name="extra_output_tab" />
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165 <output file="count-coverage.pdf" name="output_pdf" />
0
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166 </test>
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167 <test>
2
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168 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
5
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169 <param name="plots_options_selector" value="two_plot" />
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170 <param name="first_plot" value="Counts" />
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171 <param name="extra_plot" value="Size" />
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172 <param name="normalization" value="1 1" />
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173 <output file="count.tab" name="output_tab" />
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174 <output file="size.tab" name="extra_output_tab" />
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175 <output file="count-size.pdf" name="output_pdf" />
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176 </test>
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177 <test>
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178 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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179 <param name="plots_options_selector" value="two_plot" />
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180 <param name="first_plot" value="Size" />
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181 <param name="extra_plot" value="Counts" />
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182 <param name="normalization" value="1 1" />
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183 <output file="size.tab" name="output_tab" />
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184 <output file="count.tab" name="extra_output_tab" />
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185 <output file="size-count.pdf" name="output_pdf" />
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186 </test>
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187 <test>
2
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188 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
6
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189 <param name="plots_options_selector" value="two_plot" />
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190 <param name="first_plot" value="Size" />
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191 <param name="extra_plot" value="Counts" />
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192 <param name="normalization" value="1 0.75" />
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193 <output file="size.tab" name="output_tab" />
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194 <output file="count.tab" name="extra_output_tab" />
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195 <output file="size-count_normed.pdf" name="output_pdf" />
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196 </test>
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197 <test>
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198 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
5
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199 <param name="plots_options_selector" value="one_plot" />
6
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200 <param name="normalization" value="1 1" />
5
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201 <param name="first_plot" value="Counts" />
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202 <output file="count.tab" name="output_tab" />
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203 <output file="count.pdf" name="output_pdf" />
0
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204 </test>
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205 <test>
2
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206 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
5
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207 <param name="plots_options_selector" value="one_plot" />
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208 <param name="first_plot" value="Size" />
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209 <param name="normalization" value="1 1" />
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210 <output file="size.tab" name="output_tab" />
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211 <output file="size.pdf" name="output_pdf" />
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212 </test>
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213 <test>
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214 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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215 <param name="plots_options_selector" value="one_plot" />
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216 <param name="first_plot" value="Coverage" />
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217 <param name="normalization" value="1 1" />
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218 <output file="coverage.tab" name="output_tab" />
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219 <output file="coverage.pdf" name="output_pdf" />
0
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220 </test>
6
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221 <test>
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222 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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223 <param name="plots_options_selector" value="one_plot" />
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224 <param name="first_plot" value="Coverage" />
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225 <param name="normalization" value="1 0.2" />
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226 <output file="coverage.tab" name="output_tab" />
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227 <output file="coverage_normed.pdf" name="output_pdf" />
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228 </test>
0
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229 </tests>
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230
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231
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232 <help>
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233
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234 **What it does**
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235
6
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236 Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5)
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237 size read distribution along chromosome references.
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238
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239 Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads
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240 whose 5' end map to a given coordinate in a chromosome reference.
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241 Coverage depths are computed from the input bam alignment files using the python pysam module.
0
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242
6
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243 The variables mentioned above (1-5) can be plotted either separately or in all possible
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244 pairwise combinations.
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245
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246 For comparison purpose, values from bam alignment files can be normalized by a size factor
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247 before plotting. If the normalization field is leaved blank, default normalization of 1
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248 is assumed.
0
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249
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250 **Inputs**
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251
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252 bam alignment files that must be
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253
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254 - single-read
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255 - sorted
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256 - mapping to the same reference
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257
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258 Optionally, a space-separated list of normalization/size factors may be added before plotting.
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259 This list maps to the selected bam alignments from bottom to top.
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260
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261 **Output**
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262
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263 A pdf file generated by the R package lattice
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264
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265 One or two dataframes used to plot data
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266
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267 </help>
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268
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269 <citations>
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270 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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271 <citation type="bibtex">@Book{,
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272 title = {Lattice: Multivariate Data Visualization with R},
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273 author = {Deepayan Sarkar},
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274 publisher = {Springer},
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275 address = {New York},
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276 year = {2008},
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277 note = {ISBN 978-0-387-75968-5},
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278 url = {http://lmdvr.r-forge.r-project.org},
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279 }</citation>
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280 </citations>
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281 </tool>
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282