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annotate small_rna_clusters.xml @ 0:8028521b6e4f draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
author artbio
date Mon, 07 Oct 2019 12:51:25 -0400
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children 160e35e432a0
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8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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1 <tool id="small_rna_clusters" name="small_rna_clusters" version="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="0.15.3=py27hda2845c_1">pysam</requirement>
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5 <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
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6 <requirement type="package" version="0.6_28=r36h6115d3f_1002">r-latticeextra</requirement>
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7 <requirement type="package" version="2.3=r36h6115d3f_1002">r-gridextra</requirement>
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8 <requirement type="package" version="1.4.3=r36h29659fb_0">r-reshape2</requirement>
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9 <requirement type="package" version="0.6.6">sambamba</requirement>
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10 <requirement type="package" version="1.9=h10a08f8_12">samtools</requirement>
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11 <requirement type="package" version="64.2=he1b5a44_1">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 '$file.element_identifier' &&
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21 samtools index '$file.element_identifier' &&
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22 #end for
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23
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24 python '$__tool_directory__'/small_rna_clusters.py
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25 --inputs ${ ' '.join(['"%s"' % x.element_identifier for x in $inputs]) }
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26 #set $labels = list()
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27 #for $file in $inputs:
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28 $labels.append(str($file.element_identifier))
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29 #end for
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30 --sample_names ${ ' '.join(['"%s"' % x for x in $labels]) }
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31 --minsize $minsize
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32 --maxsize $maxsize
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33 --outputs '$output_tab'
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34 --cluster $cluster
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35 --bed '$output_bed'
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36 --bed_skipsize $skip_size
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37 --bed_skipcounts $skip_counts
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38 --bed_skipdensity $skip_density
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39 $strandness &&
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40
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41 Rscript '$__tool_directory__'/small_rna_clusters.r
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42 --first_dataframe '$output_tab'
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43 --first_plot_method 'Counts'
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44 --output_pdf '$output_pdf'
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45 ]]></command>
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46 <inputs>
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47 <param name="inputs" type="data" format="bam" label="Select a alignment files to parse" multiple="true"
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48 help="maps from these bam inputs will be collected in a single pdf output" />
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49 <param name="minsize" type="integer" label="Minimal size of reads for inclusion in analysis"
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50 value="19" help="default value: 19" />
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51 <param name="maxsize" type="integer" label="Maximal size of reads for inclusion in analysis"
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52 value="29" help="default value: 29" />
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53 <param name="first_plot" type="hidden" value="Counts"/>
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54 <param name="cluster" type="integer" label="Clustering distance in nucleotides" value="1"
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55 help="Sets the distance (in nt) below which reads are clustered to a single median position" />
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56 <param name="strandness" argument="--nostrand" type="boolean" truevalue="--nostrand" falsevalue="" checked="false"
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57 label="Ignore polarity of reads ?" help="Set if you wish to cluster reads regardless of whether they are forward or reverse"/>
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58 <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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59 help="Cluster size threshod (in nucleotides) for reporting. Set to 1 (default) reports all clusters, including singlets" />
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60 <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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61 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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62 <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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63 help="Density threshod (in reads per nucleotides) for reporting. Set to 0 (default) reports all cluster densities" />
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64 </inputs>
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65
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66 <outputs>
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67 <data format="tabular" name="output_tab" label="Counts Dataframe" />
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68 <data format="bed" name="output_bed" label="bed file for clusters" />
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69 <data format="pdf" name="output_pdf" label="small RNA maps" />
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70 </outputs>
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71
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72 <tests>
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73 <test> <!-- 0 -->
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74 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
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75 <param name="cluster" value="500" />
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76 <param name="skip_size" value="1" />
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77 <param name="strandness" value="false" />
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78 <output file="clustering_0.tab" name="output_tab" />
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79 <output file="clustering_0.pdf" name="output_pdf" />
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80 <output file="bed_0.bed" name="output_bed" />
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81 </test>
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82 <test> <!-- 1 -->
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artbio
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83 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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84 <param name="cluster" value="500" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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85 <param name="skip_size" value="1" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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86 <param name="strandness" value="true" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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87 <output file="clustering_1.tab" name="output_tab" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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88 <output file="clustering_1.pdf" name="output_pdf" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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89 <output file="bed_1.bed" name="output_bed" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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90 </test>
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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91 <test> <!-- 2 -->
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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92 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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93 <param name="cluster" value="500" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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94 <param name="skip_size" value="1000" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
artbio
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95 <param name="strandness" value="false" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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96 <output file="clustering_2.tab" name="output_tab" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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97 <output file="clustering_2.pdf" name="output_pdf" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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98 <output file="bed_2.bed" name="output_bed" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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99 </test>
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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100 <test> <!-- 3 -->
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101 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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102 <param name="cluster" value="500" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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103 <param name="skip_size" value="1000" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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104 <param name="skip_counts" value="200" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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105 <param name="skip_density" value="0.1" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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106 <param name="strandness" value="false" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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107 <output file="clustering_3.tab" name="output_tab" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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108 <output file="clustering_3.pdf" name="output_pdf" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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109 <output file="bed_3.bed" name="output_bed" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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110 </test>
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111 <test> <!-- 4 -->
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112 <param name="inputs" value="input1.bam,input2.bam" ftype="bam" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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113 <param name="cluster" value="2000" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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114 <param name="skip_size" value="2000" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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115 <param name="skip_counts" value="100" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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116 <param name="skip_density" value="0.1" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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117 <param name="strandness" value="true" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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118 <output file="clustering_4.tab" name="output_tab" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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119 <output file="clustering_4.pdf" name="output_pdf" />
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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120 <output file="bed_4.bed" name="output_bed" />
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121 </test>
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122 </tests>
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123 <help>
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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124 **What it does**
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125
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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126 Clusters of read alignments (provided as bam files) are aggregated along regions of
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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127 *variable* lengths. The Clustering algorithm works as follows:
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128
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129 A read is clustered with the next read on the genomic reference if the two reads are
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130 separated by *at maximum* the clustering distance (set in nucleotides). If clustered, the
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131 step is repeated with the following read until clustering fails. A new cluster is then
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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132 searched.
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133
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134 For clustering procedure, one has the possibility to consider the polarity of reads
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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135 (default setting, only forward reads or reverse reads can be clustered, separately), or to
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136 ignore this polarity.
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137
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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138 Clusters of reads are plotted as single bars, their coordinates being the medians of
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139 the flanking coordinates of the clusters.
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140
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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141 In addition, cluster are reported in a bed file. There, clusters can be filtered out upon
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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142 various parameters: cluster size, cluster read number or cluster read density (number of
8028521b6e4f "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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143 reads divided by the length of the cluster).
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144
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145 Note that bed filtering options only affect the number of reported line in the bed file.
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146 All clusters are shown in the plot. **i.e. the only parameter that affects the number of
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147 found clusters is the clustering distance.**
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148
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149 **Inputs**
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150
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151 bam alignment files that must be
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152
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153 - single-read
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154 - sorted
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155 - mapped to the same reference
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156
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157 .. class:: warningmark
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158
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159 This tools follows a "map-reduce" procedure: multiple inputs, which can be arranged in a
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160 data collection, are visualised side by side in a single pdf file and are reported in a
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161 single bed file.
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162
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163 **Output**
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164
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165 A pdf file generated by the R package lattice, a dataframe used to plot the clusters, and
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166 a bed file that reports significant clusters.
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167 </help>
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168
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169 <citations>
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170 <citation type="doi">10.1093/bioinformatics/btp352</citation>
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171 <citation type="bibtex">@Book{,
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172 title = {Lattice: Multivariate Data Visualization with R},
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173 author = {Deepayan Sarkar},
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174 publisher = {Springer},
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175 address = {New York},
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176 year = {2008},
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177 note = {ISBN 978-0-387-75968-5},
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178 url = {http://lmdvr.r-forge.r-project.org},
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179 }</citation>
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180 </citations>
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181 </tool>