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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 6dc66b89f0792e4da40719ec83494a1fcee5e105"
author artbio
date Thu, 03 Jun 2021 23:59:03 +0000
parents 3c0451ca266e
children
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9eb4a7000c1e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 6dc66b89f0792e4da40719ec83494a1fcee5e105"
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1 <tool id="probecoverage" name="Probe Coverage" version="0.7.0">
0
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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2 <description></description>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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3 <requirements>
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4 <requirement type="package" version="1.10=h9402c20_2">samtools</requirement>
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5 <requirement type="package" version="2.29.2=hc088bd4_0">bedtools</requirement>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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6 <requirement type="package" version="1.6.4=r36h6115d3f_0">r-optparse</requirement>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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7 <requirement type="package" version="3.2.1=r36h6115d3f_0">r-ggplot2</requirement>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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8 <requirement type="package" version="1.17.3=py37h95a1406_0">numpy</requirement>
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9eb4a7000c1e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 6dc66b89f0792e4da40719ec83494a1fcee5e105"
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9 <requirement type="package" version="0.16.0.1">pysam</requirement>
0
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10 </requirements>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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11 <stdio>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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12 <exit_code range="1:" level="fatal" description="Tool exception" />
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13 </stdio>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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14 <command detect_errors="exit_code"><![CDATA[
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15 #for $file in $inputs
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16 samtools index '$file' &&
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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17 #end for
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18 #if $method == 'pysam':
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19 python $__tool_directory__/multicov.py
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20 #else:
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21 bedtools multicov
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22 #end if
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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23 -bams
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24 #for $file in $inputs
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25 '$file'
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26 #end for
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27 -bed '$bed' > $coverage_dataframe &&
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28 Rscript '$__tool_directory__'/probecoverage.r
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29 --method '$method'
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30 --input '$coverage_dataframe'
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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31 --title 'Probe coverage depth (cumulative distribution)'
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32 --xlab
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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33 #if $method == 'pysam':
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34 'Depth (pysam method)'
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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35 #else:
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36 'Depth (bedtools muticov method)'
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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37 #end if
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38 --ylab 'Fraction of covered regions with coverage >= Depth'
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39 --output '$distribution'
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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40 --sample "
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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41 #for $file in $inputs
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42 $file.element_identifier,
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43 #end for
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44 "
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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45
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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46 ]]></command>
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47 <inputs>
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48 <param name="inputs" type="data" format="bam" label="Select multiple Bam alignments to parse" multiple="True"/>
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49 <param name="bed" type="data" format="bed" label="Select a bed file describing the genomic regions to analyze" />
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50 <param name="method" type="boolean" falsevalue="bedtools" checked="false" truevalue="pysam"
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51 help="coverage is computed using bedtools multicov (default) or pysam module"
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52 label="Compute coverage with pysam (bedtools by default)" />
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53 </inputs>
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54
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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55 <outputs>
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56 <data format="tabular" name="coverage_dataframe" label="coverage table" />
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57 <data format="pdf" name="distribution" label="Cumulative distribution of region coverages" />
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58 </outputs>
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59
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60 <tests>
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61 <test>
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62 <param name="inputs" value="sample1,sample2,sample3" ftype="bam"/>
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63 <param name="bed" value="probes.bed" ftype="bed"/>
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64 <param name="method" value="bedtools" />
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65 <output file="coverage.tab" name="coverage_dataframe" />
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66 <output file="graph.pdf" name="distribution" />
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67 </test>
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68 <test>
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69 <param name="inputs" value="sample1,sample2,sample3" ftype="bam"/>
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70 <param name="bed" value="probes.bed" ftype="bed"/>
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71 <param name="method" value="pysam" />
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72 <output file="coverage_pysam.tab" name="coverage_dataframe" />
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73 <output file="graph_pysam.pdf" name="distribution" />
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74 </test>
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75 </tests>
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76
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77
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78 <help>
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79
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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80 **What it does**
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81
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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82 Generates counts of alignments from multiple position-sorted BAM files
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83 that overlap intervals in a BED file.
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84
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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85 Shows data as a cumulative plot of numbers of regions with coverage > x.
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86
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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87 **Inputs**
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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88
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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89 bam alignment files that must be
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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90
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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91 - sorted
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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92 - mapped to the same reference
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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93
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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94 **Output**
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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95
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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96 A data frame of computed counts
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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97
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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98 A pdf file generated by R
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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99
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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100 </help>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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101
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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102 <citations>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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103 <citation type="doi">10.1093/bioinformatics/btq033</citation>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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104 </citations>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
artbio
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105 </tool>
3c0451ca266e "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/probecoverage commit 62a8b073b9ac98b0231641e5266768e7f8b80b89"
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106