Mercurial > repos > artbio > small_rna_maps

annotate small_rna_maps.xml @ 13:458a88317c22 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
author artbio
date Tue, 10 Apr 2018 06:12:01 -0400
parents d33263e6e812
children cd75c72e1d75
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13
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1 <tool id="small_rna_maps" name="small_rna_maps" version="2.5.1">
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>
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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[
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16 #for $file in $series
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17 samtools index '$file.inputs';
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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 $series
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22 '$file.inputs'
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23 #end for
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24 --sample_names
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25 #for $sample in $series
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26 '$sample.inputs.name'
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27 #end for
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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';
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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
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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
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45 #set $norm = ""
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46 #for $file in $series
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47 #set $norm += str($file.normalization)+' '
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48 #end for
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49 #set $norm = $norm[:-1]
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50 '$norm'
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51 #if $ylimits_cond.ylimits == "no":
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52 --ymin '' --ymax ''
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53 #else:
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54 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
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55 #end if
5
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56 #if str($plots_options.plots_options_selector ) == "two_plot":
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57 --first_plot_method '${plots_options.first_plot}'
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58 --extra_plot_method '${plots_options.extra_plot}'
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59 #elif str($plots_options.plots_options_selector ) == "global":
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60 --first_plot_method 'Size'
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61 --extra_plot_method ''
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62 --global '${plots_options.mergestrands}'
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63 #else:
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64 --first_plot_method '${plots_options.first_plot}'
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65 --extra_plot_method ''
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66 #end if
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67 --output_pdf '$output_pdf'
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68 ]]></command>
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69 <inputs>
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70 <repeat name="series" title="Input" min="1">
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71 <param name="inputs" type="data" format="bam" label="Select a single alignment file to parse" multiple="false"
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72 help="If 'multiple datasets' method is used, the same normalization factor will be applied to each dataset. Please refer to the help section for more information." />
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73 <param name="normalization" type="float" label="Enter a size/normalization factor."
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74 help="Enter only one value e.g. '0.75' or '1.23'" value="1.0"/>
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75 </repeat>
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76 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
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77 value="0" help="default value: 0" />
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78 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
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79 value="10000" help="default value: 10000" />
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80 <param name="cluster" type="integer" label="Aggregation distance in nucleotides"
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81 value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" />
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82 <conditional name="plots_options">
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83 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
5
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artbio
parents: 4
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84 <option value="one_plot">Just one plot per chromosome</option>
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artbio
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85 <option value="two_plot" selected="True">Two plots per chromosome</option>
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents: 6
diff changeset
86 <option value="global">Global read size distributions of aligned reads</option>
5
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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87 </param>
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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88 <when value="two_plot">
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
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89 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
5
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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90 <option value="Counts">Counts</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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91 <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
parents: 4
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92 <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
diff changeset
93 <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
parents: 4
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94 <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
parents: 4
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95 </param>
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
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96 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
5
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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97 <option value="Counts">Counts</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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98 <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
parents: 4
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99 <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
diff changeset
100 <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
parents: 4
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101 <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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102 </param>
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artbio
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103 </when>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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104 <when value="one_plot">
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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105 <param name="first_plot" type="select" display="radio" label="select the type of plot">
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
106 <option value="Counts">Counts</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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107 <option value="Coverage">Coverage</option>
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artbio
parents: 4
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108 <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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109 <option value="Median">Median Sizes</option>
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artbio
parents: 4
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110 <option value="Size">Size Distributions</option>
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artbio
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111 </param>
12c14642e6ac planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 24a21619d79d83b38cef7f1a7b858c621e4c8449
artbio
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112 </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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113 <when value="global">
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artbio
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114 <param name="first_plot" type="hidden" 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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115 <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
artbio
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116 <option value="nomerge">Do not merge</option>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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117 <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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118 </param>
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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119 </when>
5
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artbio
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120 </conditional>
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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121 <conditional name="ylimits_cond">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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122 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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123 help="This limit won't be applied to size distribution plots"/>
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artbio
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124 <when value="yes">
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artbio
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125 <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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126 <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/>
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127 </when>
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artbio
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128 <when value="no">
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129 </when>
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artbio
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130 </conditional>
0
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131 </inputs>
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132
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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133 <outputs>
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 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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135 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_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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136 <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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137 </data>
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 <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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139 </outputs>
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140
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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141 <tests>
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142 <test>
13
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artbio
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diff changeset
143 <repeat name="series">
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artbio
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144 <param name="inputs" value="input1.bam" ftype="bam" />
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artbio
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145 <param name="normalization" value="1.0" />
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artbio
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146 </repeat>
12
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147 <param name="minsize" value="0" />
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artbio
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148 <param name="maxsize" value="10000" />
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artbio
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149 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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150 <param name="ylimits" value="yes" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
151 <param name="ymin" value="-5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
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152 <param name="ymax" value="5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
153 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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154 <param name="first_plot" value="Counts" />
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artbio
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155 <output file="input1_counts_yminneg5_5.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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156 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
157 </test>
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artbio
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diff changeset
158 <test>
13
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artbio
parents: 12
diff changeset
159 <repeat name="series">
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artbio
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diff changeset
160 <param name="inputs" value="input1.bam" ftype="bam" />
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artbio
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diff changeset
161 <param name="normalization" value="1.0" />
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artbio
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diff changeset
162 </repeat>
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
163 <param name="minsize" value="0" />
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artbio
parents: 11
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164 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
165 <param name="cluster" value="5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
166 <param name="plots_options_selector" value="one_plot" />
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artbio
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167 <param name="first_plot" value="Coverage" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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168 <output file="input1_coverage_cluster5.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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169 <output file="input1_cluster5_single_plot_coverage.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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170 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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171 <test>
13
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artbio
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diff changeset
172 <repeat name="series">
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artbio
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173 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
174 <param name="normalization" value="1.0" />
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artbio
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175 </repeat>
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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176 <param name="minsize" value="20" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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177 <param name="maxsize" value="30" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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178 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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179 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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180 <param name="first_plot" value="Size" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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181 <output file="input1_min20_max30_size.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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182 <output file="input1_min20_max30_single_plot_size.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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183 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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184 <test>
13
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
185 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
186 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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187 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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188 </repeat>
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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189 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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190 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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191 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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192 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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193 <param name="first_plot" value="Mean" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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194 <output file="input1_mean.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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195 <output file="input1__single_plot_mean.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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196 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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197 <test>
13
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
198 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
199 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
200 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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201 </repeat>
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
202 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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203 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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204 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
205 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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206 <param name="first_plot" value="Median" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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207 <output file="input1_median.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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208 <output file="input1_single_plot_median.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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209 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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210 <test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
211 <repeat name="series">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
212 <param name="inputs" value="input1.bam" ftype="bam" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
213 <param name="normalization" value="1.0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
214 </repeat>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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215 <repeat name="series">
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
216 <param name="inputs" value="input2.bam" ftype="bam" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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217 <param name="normalization" value="2.0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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218 </repeat>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
219 <param name="minsize" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
220 <param name="maxsize" value="10000" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
221 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
222 <param name="plots_options_selector" value="one_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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223 <param name="first_plot" value="Counts" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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224 <output file="input1_input2_norm_1_2_counts.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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225 <output file="input1_input2_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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226 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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227 <test>
13
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artbio
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228 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
229 <param name="inputs" value="input1.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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230 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
231 </repeat>
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
232 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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233 <param name="inputs" value="input2.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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234 <param name="normalization" value="1.0" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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235 </repeat>
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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236 <param name="minsize" value="0" />
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artbio
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237 <param name="maxsize" value="10000" />
12
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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238 <param name="cluster" value="0" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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239 <param name="ylimits" value="yes" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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240 <param name="ymin" value="-5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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241 <param name="ymax" value="5" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
242 <param name="plots_options_selector" value="two_plot" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
243 <param name="first_plot" value="Counts" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
244 <param name="extra_plot" value="Size" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
245 <output file="input1_input2_counts.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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246 <output file="input1_input2_size.tab" name="extra_output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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247 <output file="input1_input2_double_plot_counts_size_ylimneg5_5.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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diff changeset
248 </test>
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
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249 <test>
13
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artbio
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diff changeset
250 <repeat name="series">
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
251 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
458a88317c22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c2fde4ca142c58719749c04046270479485e8d4b
artbio
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diff changeset
252 <param name="normalization" value="1.0" />
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253 </repeat>
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254 <repeat name="series">
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artbio
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255 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
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256 <param name="normalization" value="1.0" />
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257 </repeat>
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258 <repeat name="series">
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259 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
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260 <param name="normalization" value="1.0" />
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261 </repeat>
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262 <repeat name="series">
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artbio
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263 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
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artbio
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264 <param name="normalization" value="1.0" />
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265 </repeat>
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266 <repeat name="series">
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267 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
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268 <param name="normalization" value="1.0" />
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269 </repeat>
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270 <repeat name="series">
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271 <param name="inputs" value="input_single_chr.bam" ftype="bam" />
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272 <param name="normalization" value="1.0" />
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273 </repeat>
12
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274 <param name="minsize" value="0" />
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275 <param name="maxsize" value="10000" />
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276 <param name="cluster" value="0" />
9
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277 <param name="plots_options_selector" value="one_plot" />
12
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278 <param name="first_plot" value="Coverage" />
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279 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
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280 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
9
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281 </test>
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282 <test>
13
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283 <repeat name="series">
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284 <param name="inputs" value="input1.bam" ftype="bam" />
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285 <param name="normalization" value="1.0" />
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286 </repeat>
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287 <repeat name="series">
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288 <param name="inputs" value="input2.bam" ftype="bam" />
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289 <param name="normalization" value="1.0" />
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290 </repeat>
9
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291 <param name="minsize" value="0" />
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292 <param name="maxsize" value="10000" />
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293 <param name="cluster" value="0" />
7
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294 <param name="plots_options_selector" value="global" />
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295 <param name="mergestrands" value="nomerge" />
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296 <param name="first_plot" value="Size" />
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297 <output file="size.tab" name="output_tab" />
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298 <output file="global_nomerge.pdf" name="output_pdf" />
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299 </test>
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300 <test>
13
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301 <repeat name="series">
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302 <param name="inputs" value="input1.bam" ftype="bam" />
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303 <param name="normalization" value="1.0" />
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304 </repeat>
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305 <repeat name="series">
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306 <param name="inputs" value="input2.bam" ftype="bam" />
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307 <param name="normalization" value="1.0" />
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308 </repeat>
8
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309 <param name="minsize" value="0" />
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310 <param name="maxsize" value="10000" />
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311 <param name="cluster" value="0" />
7
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312 <param name="plots_options_selector" value="global" />
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313 <param name="mergestrands" value="merge" />
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314 <param name="first_plot" value="Size" />
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315 <output file="size.tab" name="output_tab" />
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316 <output file="global_merge.pdf" name="output_pdf" />
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317 </test>
0
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318 </tests>
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319 <help>
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320
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321 **What it does**
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322
12
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323 Plots mapping statistics of an alignment along the reference chromosomes :
6
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324
12
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325 - counts
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326 - mean sizes
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327 - median sizes
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328 - coverage depth
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329 - size distribution
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330
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331 Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads
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332 in each position of a chromosome reference.
6
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333 Coverage depths are computed from the input bam alignment files using the python pysam module.
0
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334
12
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335 The metrics mentioned above can be plotted either separately:
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336
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337 .. image:: one_plot.png
6
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338
12
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339 Or in all possible pairwise combinations:
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340
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341 .. image:: two_plot.png
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342
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343 For comparison purposes, values from bam alignment files can be normalized by a size factor
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344 before plotting.
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345
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346 **Inputs**
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347
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348 bam alignment files that must be
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349
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350 - single-read
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351 - sorted
12
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352 - mapped to the same reference
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353
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354 To plot 2 alignment files in the same PDF output the 'single dataset' method should be used.
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355
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356 .. class:: warningmark
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357
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358 If the 'multiple dataset' method is used the normalization factor will be applied to every file selected in the input list.
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359 Additionally each file in the selected list will be plotted in a separate PDF file.
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360
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361 **Output**
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362
12
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363 A pdf file generated by the R package lattice and one or two dataframes used to plot the data.
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364
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365 </help>
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366
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367 <citations>
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368 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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369 <citation type="bibtex">@Book{,
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370 title = {Lattice: Multivariate Data Visualization with R},
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371 author = {Deepayan Sarkar},
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372 publisher = {Springer},
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373 address = {New York},
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374 year = {2008},
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375 note = {ISBN 978-0-387-75968-5},
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376 url = {http://lmdvr.r-forge.r-project.org},
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377 }</citation>
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378 </citations>
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379 </tool>
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380