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annotate small_rna_maps.xml @ 33:6fee74f6d2bd draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 8c676ff51e50ed8c15636d9481acfbebc2f59229"
author artbio
date Mon, 25 Oct 2021 09:21:34 +0000
parents f2e7ad3058e8
children 966bc5c46efd
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6fee74f6d2bd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 8c676ff51e50ed8c15636d9481acfbebc2f59229"
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1 <tool id="small_rna_maps" name="small_rna_maps" version="3.1.0">
0
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="1.21.3=py37h31617e3_0">numpy</requirement>
6fee74f6d2bd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 8c676ff51e50ed8c15636d9481acfbebc2f59229"
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5 <requirement type="package" version="0.17.0=py37h45aed0b_0">pysam</requirement>
6fee74f6d2bd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 8c676ff51e50ed8c15636d9481acfbebc2f59229"
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6 <requirement type="package" version="1.7.1=r40hc72bb7e_0">r-optparse</requirement>
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7 <requirement type="package" version="0.6_29=r40hc72bb7e_1">r-latticeextra</requirement>
6fee74f6d2bd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 8c676ff51e50ed8c15636d9481acfbebc2f59229"
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8 <requirement type="package" version="2.3=r40hc72bb7e_1003">r-gridextra</requirement>
6fee74f6d2bd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 8c676ff51e50ed8c15636d9481acfbebc2f59229"
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9 <requirement type="package" version="1.4.4=r40h03ef668_1">r-reshape2</requirement>
6fee74f6d2bd "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 8c676ff51e50ed8c15636d9481acfbebc2f59229"
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10 <requirement type="package" version="0.8.1=h41abebc_0">sambamba</requirement>
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11 <requirement type="package" version="68.1=h58526e2_0">icu</requirement>
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12 </requirements>
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13 <stdio>
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14 <exit_code range="1:" level="fatal" description="Tool exception" />
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15 </stdio>
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16 <command detect_errors="exit_code"><![CDATA[
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17 #import json
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18 #import os
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19 #for $file in $inputs
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20 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file' -o '$file.element_identifier' &&
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21 sambamba index -t \${GALAXY_SLOTS} '$file.element_identifier' &&
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22 #end for
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23 python '$__tool_directory__'/small_rna_maps.py
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24 --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }
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25 #set $labels = list()
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26 #for $file in $inputs:
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27 $labels.append(str($file.element_identifier))
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28 #end for
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29 --sample_names ${ ' '.join(['"%s"' % x for x in $labels]) }
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30 --minsize $minsize
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31 --maxsize $maxsize
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32 #if str($plots_options.plots_options_selector ) == "two_plot":
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33 --plot_methods '${plots_options.first_plot}' '${plots_options.extra_plot}'
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34 --outputs '$output_tab' '$extra_output_tab' &&
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35 #elif str($plots_options.plots_options_selector ) == "global":
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36 --plot_methods 'Size'
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37 --outputs '$output_tab' &&
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38 #elif str($plots_options.plots_options_selector ) == "cluster":
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39 --plot_methods 'Counts'
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40 --outputs '$output_tab'
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41 --cluster ${plots_options.cluster}
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42 --bed '$output_bed'
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43 --bed_skipsize ${plots_options.skip_size}
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44 --bed_skipcounts ${plots_options.skip_counts}
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45 --bed_skipdensity ${plots_options.skip_density}
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46 ${plots_options.strandness} &&
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47 #else:
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48 --plot_methods '${plots_options.first_plot}'
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49 --outputs '$output_tab' &&
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50 #end if
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51
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52
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53 Rscript '$__tool_directory__'/small_rna_maps.r
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54 --first_dataframe '$output_tab'
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55 --extra_dataframe '$extra_output_tab'
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56 #if len(str($normalization)) != 1:
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57 --normalization "${ ' '.join( [factor for factor in $normalization.split()]) }"
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58 #else:
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59 --normalization "${ ' '.join( ["1" for factor in $inputs] )}"
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60 #end if
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61 #if $ylimits_cond.ylimits == "no":
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62 --ymin '' --ymax ''
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63 #else:
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64 --ymin '${ylimits_cond.ymin}' --ymax '${ylimits_cond.ymax}'
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65 #end if
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66 #if str($plots_options.plots_options_selector ) == "two_plot":
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67 --first_plot_method '${plots_options.first_plot}'
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68 --extra_plot_method '${plots_options.extra_plot}'
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69 #elif str($plots_options.plots_options_selector ) == "global":
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70 --first_plot_method 'Size'
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71 --extra_plot_method ''
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72 --global '${plots_options.mergestrands}'
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73 #else:
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74 --first_plot_method '${plots_options.first_plot}'
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75 --extra_plot_method ''
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76 #end if
7
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77 --output_pdf '$output_pdf'
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78 ]]></command>
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79 <inputs>
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80 <param name="inputs" type="data" format="bam" label="Select a alignment files to parse" multiple="true"
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81 help="maps from these bam inputs will be collected in a single pdf output" />
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artbio
parents: 21
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82 <param name="normalization" type="text" label="Enter a size/normalization factor."
29
8b5695592784 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c3d728b98db4987821feae40952d9797c97eaf5a"
artbio
parents: 28
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83 help="Enter normalisation factors separated by space eg [0.75 1.23 1.1], no normalization if no values,
8b5695592784 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c3d728b98db4987821feae40952d9797c97eaf5a"
artbio
parents: 28
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84 ignored if a single sample"
8b5695592784 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c3d728b98db4987821feae40952d9797c97eaf5a"
artbio
parents: 28
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85 value="1"/>
8
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artbio
parents: 7
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86 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
26
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artbio
parents: 25
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87 value="19" help="default value: 19" />
8
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artbio
parents: 7
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88 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
26
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artbio
parents: 25
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89 value="29" help="default value: 29" />
5
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artbio
parents: 4
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90 <conditional name="plots_options">
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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91 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
5
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artbio
parents: 4
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92 <option value="one_plot">Just one plot per chromosome</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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93 <option value="two_plot" selected="True">Two plots per chromosome</option>
15
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artbio
parents: 14
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94 <option value="global">Global read size distributions of aligned reads</option>
16
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artbio
parents: 15
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95 <option value="cluster">Map read clusters</option>
5
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artbio
parents: 4
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96 </param>
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artbio
parents: 4
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97 <when value="two_plot">
12
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artbio
parents: 11
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98 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
15
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artbio
parents: 14
diff changeset
99 <option value="Counts">Counts</option>
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artbio
parents: 14
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100 <option value="Coverage">Coverage</option>
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artbio
parents: 14
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101 <option value="Mean">Mean Sizes</option>
5
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artbio
parents: 4
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102 <option value="Median">Median Sizes</option>
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artbio
parents: 4
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103 <option value="Size">Size Distributions</option>
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artbio
parents: 4
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104 </param>
12
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artbio
parents: 11
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105 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
15
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artbio
parents: 14
diff changeset
106 <option value="Counts">Counts</option>
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artbio
parents: 14
diff changeset
107 <option value="Coverage">Coverage</option>
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artbio
parents: 14
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108 <option value="Mean">Mean Sizes</option>
5
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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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parents: 4
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111 </param>
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artbio
parents: 4
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112 </when>
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artbio
parents: 4
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113 <when value="one_plot">
12
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artbio
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114 <param name="first_plot" type="select" display="radio" label="select the type of plot">
15
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artbio
parents: 14
diff changeset
115 <option value="Counts">Counts</option>
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artbio
parents: 14
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116 <option value="Coverage">Coverage</option>
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artbio
parents: 14
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117 <option value="Mean">Mean Sizes</option>
5
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artbio
parents: 4
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118 <option value="Median">Median Sizes</option>
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artbio
parents: 4
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119 <option value="Size">Size Distributions</option>
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120 </param>
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artbio
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121 </when>
7
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artbio
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diff changeset
122 <when value="global">
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artbio
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diff changeset
123 <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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diff changeset
124 <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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diff changeset
125 <option value="nomerge">Do not merge</option>
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artbio
parents: 6
diff changeset
126 <option value="merge">Merge forward and reverse reads</option>
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artbio
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diff changeset
127 </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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diff changeset
128 </when>
16
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artbio
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diff changeset
129 <when value="cluster">
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artbio
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130 <param name="first_plot" type="hidden" value="Counts"/>
20
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131 <param name="cluster" type="integer" label="Clustering distance in nucleotides" value="1"
16
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132 help="Sets the distance (in nt) below which reads are clustered to a single median position" />
17
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artbio
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133 <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false"
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134 label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/>
20
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135 <param name="skip_size" type="integer" label="do not report clusters whose size is less than the specified value" value="1"
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artbio
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136 help="Cluster size threshod (in nucleotides) for reporting. Set to 1 (default) reports all clusters, including singlets" />
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artbio
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137 <param name="skip_counts" type="integer" label="do not report cluster with a number of reads lower than the specified value" value="1"
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artbio
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138 help="Number-of-reads threshod (in nucleotides) for cluster reporting. Set to 1 (default) reports all clusters, irrespective of their counts" />
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artbio
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139 <param name="skip_density" type="float" label="do not report cluster with density equal or less than the specified value" value="0"
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140 help="Density threshod (in reads per nucleotides) for reporting. Set to 0 (default) reports all cluster densities" />
16
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141 </when>
5
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142 </conditional>
12
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143 <conditional name="ylimits_cond">
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144 <param name="ylimits" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Do you wish to set an y axis limit to the plots?"
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145 help="This limit won't be applied to size distribution plots"/>
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146 <when value="yes">
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147 <param name="ymin" type="float" label="Enter minimum value" value="0.0" help="e.g. '-5.0'"/>
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148 <param name="ymax" type="float" label="Enter maximum value" value="0.0" help="e.g. '5.0'"/>
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149 </when>
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150 <when value="no">
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151 </when>
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152 </conditional>
0
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153 </inputs>
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154
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155 <outputs>
7
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diff changeset
156 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
18
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diff changeset
157 <data format="bed" name="output_bed" label="bed file for clusters" >
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158 <filter>plots_options['plots_options_selector'] == 'cluster'</filter>
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159 </data>
7
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artbio
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diff changeset
160 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
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161 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
15
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diff changeset
162 </data>
7
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
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163 <data format="pdf" name="output_pdf" label="small RNA maps" />
0
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164 </outputs>
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165
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166 <tests>
17
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167 <test> <!-- 0 -->
22
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168 <param name="inputs" value="input1.bam,input_new2.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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169 <param name="normalization" value="1 2" />
15
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170 <param name="plots_options_selector" value="one_plot" />
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171 <param name="first_plot" value="Counts" />
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172 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
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173 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
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174 </test>
17
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175 <test> <!-- 1 -->
22
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176 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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177 <param name="normalization" value="1.0" />
12
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178 <param name="ylimits" value="yes" />
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179 <param name="ymin" value="-5" />
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180 <param name="ymax" value="5" />
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181 <param name="plots_options_selector" value="one_plot" />
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182 <param name="first_plot" value="Counts" />
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183 <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
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184 <output file="input1_yminneg5_5_single_plot_counts.pdf" name="output_pdf" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
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185 </test>
17
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186 <test> <!-- 2 -->
22
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187 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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188 <param name="normalization" value="1.0" />
17
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189 <param name="plots_options_selector" value="cluster" />
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190 <param name="first_plot" value="Counts" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
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191 <param name="cluster" value="5" />
20
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192 <param name="skip_size" value="1" />
17
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193 <param name="strandness" value="false" />
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194 <output file="clustering.tab" name="output_tab" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
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195 <output file="clustering.pdf" name="output_pdf" />
18
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196 <output file="bed1.bed" name="output_bed" />
17
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197 </test>
16
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198 <test> <!-- 3 -->
22
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199 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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200 <param name="normalization" value="1.0" />
16
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201 <param name="plots_options_selector" value="cluster" />
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202 <param name="first_plot" value="Counts" />
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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203 <param name="cluster" value="5" />
20
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204 <param name="skip_size" value="1" />
17
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205 <param name="strandness" value="true" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
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206 <output file="clustering_unstranded.tab" name="output_tab" />
b28dcd4051e8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 16f15e5ab2b79590a8ae410f76434aa6690c1fc4
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207 <output file="clustering_unstranded.pdf" name="output_pdf" />
18
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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208 <output file="bed2.bed" name="output_bed" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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209 </test>
20
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210 <test> <!-- 4 -->
22
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artbio
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211 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
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212 <param name="normalization" value="1.0" />
18
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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213 <param name="plots_options_selector" value="cluster" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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214 <param name="first_plot" value="Counts" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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215 <param name="cluster" value="5" />
20
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216 <param name="skip_size" value="2" />
18
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217 <param name="strandness" value="false" />
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218 <output file="clustering.tab" name="output_tab" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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219 <output file="clustering.pdf" name="output_pdf" />
2c95c899d0a4 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06c6feefeaaa66f7dec1f6143a2c5aaf91836320
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220 <output file="bed3.bed" name="output_bed" />
12
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221 </test>
20
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222 <test> <!-- 5 -->
22
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223 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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224 <param name="normalization" value="1.0" />
20
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225 <param name="plots_options_selector" value="cluster" />
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226 <param name="first_plot" value="Counts" />
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227 <param name="cluster" value="5" />
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228 <param name="skip_size" value="2" />
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229 <param name="skip_counts" value="3" />
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230 <param name="skip_density" value="1.0" />
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231 <param name="strandness" value="false" />
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232 <output file="clustering.tab" name="output_tab" />
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233 <output file="clustering.pdf" name="output_pdf" />
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234 <output file="bed4.bed" name="output_bed" />
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235 </test>
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236 <test> <!-- 6 -->
22
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237 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
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238 <param name="normalization" value="1.0" />
20
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239 <param name="plots_options_selector" value="cluster" />
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240 <param name="first_plot" value="Counts" />
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241 <param name="cluster" value="5" />
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242 <param name="skip_size" value="2" />
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243 <param name="skip_counts" value="2" />
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244 <param name="skip_density" value="0.4" />
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245 <param name="strandness" value="true" />
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246 <output file="clustering_unstranded.tab" name="output_tab" />
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247 <output file="clustering_unstranded.pdf" name="output_pdf" />
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
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diff changeset
248 <output file="bed5.bed" name="output_bed" />
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
249 </test>
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
250 <test> <!-- 7 -->
22
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
251 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
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diff changeset
252 <param name="normalization" value="1.0" />
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
253 <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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diff changeset
254 <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
parents: 11
diff changeset
255 <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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diff changeset
256 <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
parents: 11
diff changeset
257 </test>
20
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
258 <test> <!-- 8 -->
22
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
259 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
260 <param name="normalization" value="1.0" />
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
261 <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
parents: 11
diff changeset
262 <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
parents: 11
diff changeset
263 <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
parents: 11
diff changeset
264 <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
parents: 11
diff changeset
265 </test>
20
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
266 <test> <!-- 9 -->
22
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
267 <param name="inputs" value="input1.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
268 <param name="normalization" value="1.0" />
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
269 <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
parents: 11
diff changeset
270 <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
parents: 11
diff changeset
271 <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
parents: 11
diff changeset
272 <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
parents: 11
diff changeset
273 </test>
20
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
274 <test> <!-- 10 -->
22
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
275 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
276 <param name="normalization" value="1.0 2.0" />
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
277 <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
parents: 11
diff changeset
278 <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
parents: 11
diff changeset
279 <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
parents: 11
diff changeset
280 <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
parents: 11
diff changeset
281 </test>
20
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
282 <test> <!-- 11 -->
22
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
283 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
284 <param name="normalization" value="1.0 1.0" />
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
285 <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
286 <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
diff changeset
287 <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
parents: 11
diff changeset
288 <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
parents: 11
diff changeset
289 <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
parents: 11
diff changeset
290 <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
parents: 11
diff changeset
291 <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
parents: 11
diff changeset
292 <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
parents: 11
diff changeset
293 <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
parents: 11
diff changeset
294 </test>
20
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
295 <test> <!-- 12 -->
22
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
296 <param name="inputs" value="input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam,input_single_chr.bam" ftype="bam" />
29f03c13c7a2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit da30f7ecca2dff1124a0c14c60f5ddb7731ccd37
artbio
parents: 21
diff changeset
297 <param name="normalization" value="1.0 1.0 1.0 1.0 1.0 1.0" />
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
298 <param name="plots_options_selector" value="one_plot" />
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
299 <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
parents: 11
diff changeset
300 <output file="input_single_chr_x_6_single_plot_coverage.tab" name="output_tab" />
d33263e6e812 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b0676fd329c2ca50002f9f2fede531d8e550569f
artbio
parents: 11
diff changeset
301 <output file="input_single_chr_x_6_single_plot_coverage.pdf" name="output_pdf" />
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
302 </test>
20
de7fbcb1348c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 44599c93586bc909f405ac6b745230563b290ee2
artbio
parents: 19
diff changeset
303 <test> <!-- 13 -->
30
183bf49fe77c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d280e9be7cf96f4938a73ccf5985533109f3328f"
artbio
parents: 29
diff changeset
304 <param name="inputs" value="size1.bam,size2.bam" ftype="bam" />
31
f82badb66c34 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"
artbio
parents: 30
diff changeset
305 <param name="normalization" value="1.0 2.5" />
f82badb66c34 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"
artbio
parents: 30
diff changeset
306 <param name="plots_options_selector" value="one_plot" />
f82badb66c34 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"
artbio
parents: 30
diff changeset
307 <param name="first_plot" value="Coverage" />
f82badb66c34 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"
artbio
parents: 30
diff changeset
308 <output file="coverage.tab" name="output_tab" />
f82badb66c34 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"
artbio
parents: 30
diff changeset
309 <output file="coverage.pdf" name="output_pdf" />
f82badb66c34 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"
artbio
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diff changeset
310 </test>
f82badb66c34 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"
artbio
parents: 30
diff changeset
311 <test> <!-- 14 -->
f82badb66c34 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"
artbio
parents: 30
diff changeset
312 <param name="inputs" value="size1.bam,size2.bam" ftype="bam" />
30
183bf49fe77c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d280e9be7cf96f4938a73ccf5985533109f3328f"
artbio
parents: 29
diff changeset
313 <param name="normalization" value="2.0 1.0" />
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
314 <param name="plots_options_selector" value="global" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents: 6
diff changeset
315 <param name="mergestrands" value="nomerge" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
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diff changeset
316 <param name="first_plot" value="Size" />
30
183bf49fe77c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d280e9be7cf96f4938a73ccf5985533109f3328f"
artbio
parents: 29
diff changeset
317 <output file="size12.tab" name="output_tab" />
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
318 <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
artbio
parents: 6
diff changeset
319 </test>
31
f82badb66c34 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7e2694ed482bd75245793e2cfe0b5277233047c3"
artbio
parents: 30
diff changeset
320 <test> <!-- 15 -->
30
183bf49fe77c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d280e9be7cf96f4938a73ccf5985533109f3328f"
artbio
parents: 29
diff changeset
321 <param name="inputs" value="size1.bam,size2.bam" ftype="bam" />
183bf49fe77c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d280e9be7cf96f4938a73ccf5985533109f3328f"
artbio
parents: 29
diff changeset
322 <param name="normalization" value="2.0 1.0" />
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
323 <param name="plots_options_selector" value="global" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents: 6
diff changeset
324 <param name="mergestrands" value="merge" />
a96e6a7df2b7 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 06472d1bd1365e4f7b385d578a69f4646481e22f
artbio
parents: 6
diff changeset
325 <param name="first_plot" value="Size" />
30
183bf49fe77c "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d280e9be7cf96f4938a73ccf5985533109f3328f"
artbio
parents: 29
diff changeset
326 <output file="size12.tab" name="output_tab" />
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
327 <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
artbio
parents: 6
diff changeset
328 </test>
0
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329 </tests>
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330 <help>
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331
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332 **What it does**
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333
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334 Plots mapping statistics of read alignments along reference chromosomes or genes or arbitrary regions :
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335
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336 - counts
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337 - mean sizes
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338 - median sizes
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339 - coverage depth
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340 - size distribution
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341
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342 Read counts, mean sizes and median sizes are computed by counting the number of 5' end of reads
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343 in each position of a chromosome reference.
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344 Coverage depths are computed from the input bam alignment files using the python pysam module.
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345
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346 The metrics mentioned above can be plotted either separately:
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347
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348 .. image:: one_plot.png
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349
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350 Or in all possible pairwise combinations:
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351
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352 .. image:: two_plot.png
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353
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354 For comparison purposes, values from bam alignment files can be normalized by a size factor
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355 before plotting (Normalisation field)
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356
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357 *Cluster mode*
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358
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359 Cluster of read alignments are aggregated along regions of *variable* lengths. The Clustering
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360 algorithm works as follows:
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361
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362 A read is clustered with the following read on the genomic reference if the two reads are
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363 separated by at maximum the clustering distance (set in nucleotides). If clustered, the step is
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364 repeated with the following read until clustering fails. A new cluster is then searched.
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365
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366 For clustering procedure, one has the possibility to consider the polarity of reads (only forward
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367 reads or reverse reads can be clustered separately), or to ignore this polarity.
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368
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369 Cluster reads are plotted as for single reads, their coordinate being the median of extrem coordinates of the cluster.
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370
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371 In addition, cluster are reported in a bed file, where clusters can be filtered out upon various parameters,
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372 cluster size, cluster read number or cluster read density (number of reads divided by the length of the cluster).
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373
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374 **Inputs**
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375
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376 bam alignment files that must be
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377
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378 - single-read
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379 - sorted
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380 - mapped to the same reference
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381
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382 .. class:: warningmark
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383
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384 This tools follows a "map-reduce" procedure: multiple inputs, that can be arranged as a data collection,
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385 are visualised side by side in a single pdf file.
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386
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387
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388
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389 **Output**
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390
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391 A pdf file generated by the R package lattice and one or two dataframes used to plot the data.
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392
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393 </help>
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394
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395 <citations>
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396 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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397 <citation type="bibtex">@Book{,
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398 title = {Lattice: Multivariate Data Visualization with R},
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399 author = {Deepayan Sarkar},
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400 publisher = {Springer},
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401 address = {New York},
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402 year = {2008},
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403 note = {ISBN 978-0-387-75968-5},
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404 url = {http://lmdvr.r-forge.r-project.org},
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405 }</citation>
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406 </citations>
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407 </tool>