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annotate small_rna_maps.xml @ 10:c3fb2a864526 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6eb3992d56ee12b901b278f2a07bed719c5d0675
author artbio
date Tue, 07 Nov 2017 17:38:39 -0500
parents 3ea75c573429
children a561a71bd7d7
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10
c3fb2a864526 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6eb3992d56ee12b901b278f2a07bed719c5d0675
artbio
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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.4.1">
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
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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 --cluster $cluster
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31 #if str($plots_options.plots_options_selector ) == "two_plot":
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32 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
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33 --outputs '$output_tab' '$extra_output_tab' &&
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34 #elif str($plots_options.plots_options_selector ) == "global":
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35 --plot_methods 'Size'
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36 --outputs '$output_tab' &&
5
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37 #else:
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38 --plot_methods '${plots_options.first_plot}'
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39 --outputs '$output_tab' &&
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40 #end if
2
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41 Rscript '$__tool_directory__'/small_rna_maps.r
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42 --first_dataframe '$output_tab'
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43 --extra_dataframe '$extra_output_tab'
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44 --normalization '$normalization'
5
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45 #if str($plots_options.plots_options_selector ) == "two_plot":
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46 --first_plot_method '${plots_options.first_plot}'
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47 --extra_plot_method '${plots_options.extra_plot}'
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48 #elif str($plots_options.plots_options_selector ) == "global":
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49 --first_plot_method 'Size'
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50 --extra_plot_method ''
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51 --global '${plots_options.mergestrands}'
5
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52 #else:
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53 --first_plot_method '${plots_options.first_plot}'
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54 --extra_plot_method ''
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55 #end if
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56 --output_pdf '$output_pdf'
0
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57 ]]></command>
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58 <inputs>
5
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59 <param name="inputs" type="data" format="bam" label="Select multiple alignments to parse" multiple="True"/>
6
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60 <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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61 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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62 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
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63 value="0" help="default value: 0" />
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64 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
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65 value="10000" help="default value: 10000" />
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66 <param name="cluster" type="integer" label="aggregation distance in nucleotides"
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67 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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68 <conditional name="plots_options">
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69 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
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70 <option value="one_plot">Just one plot per chromosome</option>
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71 <option value="two_plot" selected="True">Two plots per chromosome</option>
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72 <option value="global">Global read size distributions of aligned reads</option>
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73 </param>
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74 <when value="two_plot">
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75 <param name="first_plot" type="select" display="radio" label="Select the type of the first plot">
5
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76 <option value="Counts">Counts</option>
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77 <option value="Coverage">Coverage</option>
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78 <option value="Mean">Mean Sizes</option>
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79 <option value="Median">Median Sizes</option>
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80 <option value="Size">Size Distributions</option>
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81 </param>
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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82 <param name="extra_plot" type="select" display="radio" label="Select the type of the second plot">
5
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artbio
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83 <option value="Counts">Counts</option>
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artbio
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84 <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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85 <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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86 <option value="Median">Median 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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87 <option value="Size">Size Distributions</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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88 </param>
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artbio
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89 </when>
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artbio
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90 <when value="one_plot">
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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91 <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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92 <option value="Counts">Counts</option>
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artbio
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93 <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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94 <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
parents: 4
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95 <option value="Median">Median Sizes</option>
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artbio
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96 <option value="Size">Size Distributions</option>
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97 </param>
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98 </when>
7
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artbio
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99 <when value="global">
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artbio
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100 <param name="first_plot" type="hidden" value="Size"/>
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artbio
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101 <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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102 <option value="nomerge">Do not merge</option>
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artbio
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103 <option value="merge">Merge forward and reverse reads</option>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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104 </param>
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105 </when>
5
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106 </conditional>
0
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107 </inputs>
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108
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109 <outputs>
7
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110 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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111 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
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112 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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113 </data>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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114 <data format="pdf" name="output_pdf" label="small RNA maps" />
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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115 </outputs>
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116
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117 <tests>
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artbio
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118 <test>
2
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artbio
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119 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
8
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120 <param name="minsize" value="0" />
9
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121 <param name="cluster" value="5" />
8
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122 <param name="maxsize" value="10000" />
9
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artbio
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123 <param name="plots_options_selector" value="one_plot" />
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artbio
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124 <param name="normalization" value="1 1" />
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artbio
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125 <param name="first_plot" value="Counts" />
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artbio
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126 <output file="count_cluster_5.tab" name="output_tab" />
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artbio
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127 <output file="count_cluster_5.pdf" name="output_pdf" />
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128 </test>
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129 <test>
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artbio
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130 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
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diff changeset
131 <param name="minsize" value="0" />
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artbio
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132 <param name="maxsize" value="10000" />
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diff changeset
133 <param name="cluster" value="0" />
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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134 <param name="plots_options_selector" value="global" />
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artbio
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135 <param name="mergestrands" value="nomerge" />
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artbio
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136 <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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137 <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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138 <output file="size.tab" name="output_tab" />
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artbio
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139 <output file="global_nomerge.pdf" name="output_pdf" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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140 </test>
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artbio
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141 <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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142 <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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143 <param name="minsize" value="0" />
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144 <param name="maxsize" value="10000" />
9
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145 <param name="cluster" value="0" />
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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146 <param name="plots_options_selector" value="global" />
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artbio
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147 <param name="mergestrands" value="merge" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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148 <param name="first_plot" value="Size" />
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artbio
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149 <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
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150 <output file="size.tab" name="output_tab" />
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artbio
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151 <output file="global_merge.pdf" name="output_pdf" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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152 </test>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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153 <test>
8
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diff changeset
154 <param name="inputs" value="input1.bam" ftype="bam"/>
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artbio
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155 <param name="minsize" value="20" />
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156 <param name="maxsize" value="30" />
9
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artbio
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diff changeset
157 <param name="cluster" value="0" />
8
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diff changeset
158 <param name="plots_options_selector" value="global" />
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artbio
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159 <param name="mergestrands" value="merge" />
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artbio
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diff changeset
160 <param name="first_plot" value="Size" />
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artbio
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161 <param name="normalization" value="1 1" />
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162 <output file="size20-30.tab" name="output_tab" />
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artbio
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163 <output file="global_merge_20-30.pdf" name="output_pdf" />
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164 </test>
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165 <test>
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents: 6
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166 <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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167 <param name="minsize" value="0" />
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artbio
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168 <param name="maxsize" value="10000" />
9
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
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169 <param name="cluster" value="0" />
5
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artbio
parents: 4
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170 <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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171 <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
artbio
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172 <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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diff changeset
173 <param name="normalization" value="1 1" />
5
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artbio
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174 <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
parents: 1
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175 <output file="mean.tab" name="extra_output_tab" />
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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176 <output file="count-mean.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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177 </test>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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178 <test>
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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179 <param name="inputs" value="input2.bam,input1.bam" ftype="bam"/>
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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180 <param name="minsize" value="20" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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181 <param name="maxsize" value="30" />
9
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
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182 <param name="cluster" value="0" />
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
183 <param name="plots_options_selector" value="two_plot" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents: 7
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184 <param name="first_plot" value="Counts" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents: 7
diff changeset
185 <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
parents: 7
diff changeset
186 <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
parents: 7
diff changeset
187 <output file="count20-30.tab" name="output_tab" />
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
188 <output file="mean20-30.tab" name="extra_output_tab" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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189 <output file="count-mean-20-30.pdf" name="output_pdf" />
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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190 </test>
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
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191 <test>
2
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
192 <param name="inputs" value="input1.bam,input1.bam" ftype="bam"/>
8
1827b74f872b planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit e4588eb6c329e4516e9bcfa084a383be81b55c60
artbio
parents: 7
diff changeset
193 <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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diff changeset
194 <param name="maxsize" value="10000" />
9
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents: 8
diff changeset
195 <param name="cluster" value="0" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents: 4
diff changeset
196 <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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diff changeset
197 <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
artbio
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198 <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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diff changeset
199 <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
parents: 4
diff changeset
200 <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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diff changeset
201 <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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diff changeset
202 <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
artbio
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diff changeset
203 </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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204 <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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diff changeset
205 <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
parents: 7
diff changeset
206 <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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diff changeset
207 <param name="maxsize" value="10000" />
9
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents: 8
diff changeset
208 <param name="cluster" value="0" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents: 4
diff changeset
209 <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
parents: 4
diff changeset
210 <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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diff changeset
211 <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
parents: 5
diff changeset
212 <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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diff changeset
213 <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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diff changeset
214 <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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diff changeset
215 <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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diff changeset
216 </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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diff changeset
217 <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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diff changeset
218 <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
219 <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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diff changeset
220 <param name="maxsize" value="10000" />
9
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents: 8
diff changeset
221 <param name="cluster" value="0" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents: 4
diff changeset
222 <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
parents: 4
diff changeset
223 <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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diff changeset
224 <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
225 <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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diff changeset
226 <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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227 <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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228 <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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229 </test>
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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230 <test>
2
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
parents: 1
diff changeset
231 <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
232 <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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233 <param name="maxsize" value="10000" />
9
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents: 8
diff changeset
234 <param name="cluster" value="0" />
5
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
parents: 4
diff changeset
235 <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
parents: 4
diff changeset
236 <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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237 <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
artbio
parents: 5
diff changeset
238 <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
parents: 4
diff changeset
239 <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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diff changeset
240 <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
artbio
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diff changeset
241 <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
artbio
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diff changeset
242 </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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diff changeset
243 <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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diff changeset
244 <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
parents: 7
diff changeset
245 <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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diff changeset
246 <param name="maxsize" value="10000" />
9
3ea75c573429 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 6199193c7fe2cb56403eea8af0b40d44f7311fd5
artbio
parents: 8
diff changeset
247 <param name="cluster" value="0" />
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="two_plot" />
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249 <param name="first_plot" value="Size" />
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250 <param name="extra_plot" value="Counts" />
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251 <param name="normalization" value="1 1" />
5
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252 <output file="size.tab" name="output_tab" />
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253 <output file="count.tab" name="extra_output_tab" />
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254 <output file="size-count.pdf" name="output_pdf" />
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255 </test>
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256 <test>
2
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257 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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258 <param name="minsize" value="0" />
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259 <param name="maxsize" value="10000" />
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260 <param name="cluster" value="0" />
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261 <param name="plots_options_selector" value="two_plot" />
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262 <param name="first_plot" value="Size" />
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263 <param name="extra_plot" value="Counts" />
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264 <param name="normalization" value="1 0.75" />
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265 <output file="size.tab" name="output_tab" />
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266 <output file="count.tab" name="extra_output_tab" />
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267 <output file="size-count_normed.pdf" name="output_pdf" />
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268 </test>
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269 <test>
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270 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
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271 <param name="minsize" value="0" />
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272 <param name="cluster" value="0" />
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273 <param name="maxsize" value="10000" />
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274 <param name="plots_options_selector" value="one_plot" />
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275 <param name="normalization" value="1 1" />
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276 <param name="first_plot" value="Counts" />
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277 <output file="count.tab" name="output_tab" />
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278 <output file="count.pdf" name="output_pdf" />
0
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279 </test>
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280 <test>
2
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281 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
8
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282 <param name="minsize" value="0" />
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283 <param name="maxsize" value="10000" />
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284 <param name="cluster" value="0" />
5
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285 <param name="plots_options_selector" value="one_plot" />
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286 <param name="first_plot" value="Size" />
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287 <param name="normalization" value="1 1" />
5
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288 <output file="size.tab" name="output_tab" />
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289 <output file="size.pdf" name="output_pdf" />
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290 </test>
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291 <test>
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292 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
8
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293 <param name="minsize" value="0" />
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294 <param name="maxsize" value="10000" />
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295 <param name="cluster" value="0" />
5
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296 <param name="plots_options_selector" value="one_plot" />
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297 <param name="first_plot" value="Coverage" />
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298 <param name="normalization" value="1 1" />
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299 <output file="coverage.tab" name="output_tab" />
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300 <output file="coverage.pdf" name="output_pdf" />
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301 </test>
6
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302 <test>
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303 <param name="inputs" value="input1.bam,input2.bam" ftype="bam"/>
8
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304 <param name="minsize" value="0" />
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305 <param name="maxsize" value="10000" />
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306 <param name="cluster" value="0" />
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307 <param name="plots_options_selector" value="one_plot" />
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308 <param name="first_plot" value="Coverage" />
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309 <param name="normalization" value="1 0.2" />
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310 <output file="coverage.tab" name="output_tab" />
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311 <output file="coverage_normed.pdf" name="output_pdf" />
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312 </test>
0
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313 </tests>
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314
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315
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316 <help>
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317
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318 **What it does**
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319
6
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320 Plots maps of (1) read counts, (2) mean sizes, (3) median sizes, (4) coverage depth or (5)
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321 size read distribution along chromosome references.
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322
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323 Mean sizes and median sizes are the mean and the median sizes, respectively, of all reads
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324 whose 5' end map to a given coordinate in a chromosome reference.
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325 Coverage depths are computed from the input bam alignment files using the python pysam module.
0
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326
6
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327 The variables mentioned above (1-5) can be plotted either separately or in all possible
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328 pairwise combinations.
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329
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330 For comparison purpose, values from bam alignment files can be normalized by a size factor
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331 before plotting. If the normalization field is leaved blank, default normalization of 1
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332 is assumed.
0
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333
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334 **Inputs**
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335
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336 bam alignment files that must be
0
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337
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338 - single-read
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339 - sorted
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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340 - mapping to the same reference
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341
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342 Optionally, a space-separated list of normalization/size factors may be added before plotting.
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343 This list maps to the selected bam alignments from bottom to top.
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344
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345 **Output**
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346
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347 A pdf file generated by the R package lattice
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348
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349 One or two dataframes used to plot data
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350
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351 </help>
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352
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353 <citations>
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354 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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355 <citation type="bibtex">@Book{,
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356 title = {Lattice: Multivariate Data Visualization with R},
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357 author = {Deepayan Sarkar},
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358 publisher = {Springer},
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359 address = {New York},
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360 year = {2008},
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361 note = {ISBN 978-0-387-75968-5},
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362 url = {http://lmdvr.r-forge.r-project.org},
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363 }</citation>
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364 </citations>
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365 </tool>
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366