Mercurial > repos > iuc > qualimap_bamqc

annotate qualimap_bamqc.xml @ 0:ac607906f10a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
author iuc
date Thu, 10 Oct 2019 17:42:04 -0400
parents
children 4a89c6f84425
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ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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2 <macros>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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3 <import>qualimap_macros.xml</import>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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4 </macros>
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5 <expand macro="requirements" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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6 <expand macro="version_command" />
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7 <command detect_errors="exit_code"><![CDATA[
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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8 #import os
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9 @SET_JAVA_OPTS@ &&
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10
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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11 ## Set some default file names and paths
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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12 ## where we expect tool output to end up.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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13 ## Note that most of these need to be overwritten if the user is
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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14 ## interested in regions *outside* those defined in a custom regions
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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15 ## file.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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16 #set $out_dir = 'results'
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17 #set $report_name = 'qualimapReport'
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18 #set $summary_report = 'genome_results.txt'
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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19 #set $coverage_file = os.path.join($out_dir, 'coverage.txt')
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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20 ## This is the only file path that qualimap does not calculate
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21 ## from $out_dir.
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22 #set $per_base_coverage_target = $coverage_file
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23
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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24 qualimap bamqc
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25 -bam '$input1' -outdir results -outformat html
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26 --collect-overlap-pairs
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27 #if str($stats_regions.region_select) == 'custom_regions':
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28 -gff ${stats_regions.regions}
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29 #if $stats_regions.outside_stats:
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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30 #set $report_name = 'qualimapReportOutsideRegions'
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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31 #set $summary_report = 'outside_results.txt'
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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32 #set $coverage_file = os.path.join(
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33 $out_dir, 'outside_coverage.txt'
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34 )
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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35 #if $per_base_coverage:
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36 #set $per_base_coverage_target = '/dev/null'
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37 #end if
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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38 ${stats_regions.outside_stats}
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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39 #end if
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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40 #end if
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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41 #if $per_base_coverage:
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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42 $per_base_coverage $per_base_coverage_target
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43 #end if
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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44 -nw ${plot_specific.n_bins}
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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45 ${plot_specific.paint_chromosome_limits}
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46 #if $plot_specific.genome_gc_distr:
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47 --genome-gc-distr ${plot_specific.genome_gc_distr}
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48 #end if
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49 -hm ${plot_specific.homopolymer_size}
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50
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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51 #if $duplicate_skipping:
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52 --skip-duplicated
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53 #if str($duplicate_skipping) == '0,1':
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54 --skip-dup-mode 2
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55 #else:
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56 --skip-dup-mode ${duplicate_skipping}
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57 #end if
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58 #end if
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59 -nt \${GALAXY_SLOTS:-1} &&
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60
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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61 #if $per_base_coverage:
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62 mv $coverage_file '$output_per_base_coverage' &&
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63 #end if
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64 @MASSAGE_OUTPUT@
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65 ]]></command>
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66 <inputs>
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67 <param argument="-bam" name="input1" type="data" format="bam"
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68 label="Mapped reads input dataset" />
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69 <conditional name="stats_regions">
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70 <param name="region_select" type="select" label="Reference genome regions to calculate mapping statistics for">
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71 <option value="all">All (whole genome)</option>
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72 <option value="custom_regions">Select regions</option>
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73 </param>
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74 <when value="all" />
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75 <when value="custom_regions">
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76 <param argument="-gff" name="regions" type="data" format="gff,gtf,bed"
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77 label="Dataset specifying regions" />
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78 <param argument="-os" name="outside_stats" type="boolean" truevalue="--outside-stats" falsevalue="" checked="false"
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79 label="Invert regions"
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80 help="If selected, report read statistics *outside* the regions in the regions file." />
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81 </when>
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82 </conditional>
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83 <param argument="-oc" name="per_base_coverage" type="boolean" truevalue="--output-genome-coverage" falsevalue="" checked="false"
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84 label="Generate per-base coverage output"
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85 help="Produce additional tabular output listing the coverage at every site (omitting only zero-coverage positions) in the selected regions of the genome. Caution: Will generate a huge dataset for anything but small input genomes or restricted regions!" />
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86 <param argument="--skip-dup-mode" name="duplicate_skipping" type="select" display="checkboxes" multiple="true" optional="true"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
87 label="Skip duplicate reads">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
88 <option value="0" selected="true">Reads flagged as duplicates in input</option>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
89 <option value="1">Duplicates detected by Qualimap</option>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
90 </param>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
91 <section name="plot_specific" title="Settings affecting specific plots" expanded="false">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
92 <param argument="-nw" name="n_bins" type="integer" value="400"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
93 label="Number of bins to use in across-reference plots"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
94 help="Affected plots: Coverage, Mapping Quality and Insert Size across reference, Mapped reads GC-content distribution; the value determines the resolution of the affected plots. Note: The lower the value, the higher the memory usage of the tool!" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
95 <param argument="-c" name="paint_chromosome_limits" type="boolean" truevalue="--paint-chromosome-limits" falsevalue="" checked="true"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
96 label="Draw chromosome limits"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
97 help="Affected plots: Coverage, Mapping Quality and Insert Size across reference; in across-reference plots, indicate chromosome boundaries with dotted lines and labels" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
98 <param argument="-gd" name="genome_gc_distr" type="select" optional="true"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
99 label="Plot expected GC-content distribution of the following reference genome"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
100 help="Affected plot: Mapped reads GC-content distribution; include a precalculated GC-content distribution for the selected (Qualimap-supported) reference genome in the plot">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
101 <option value="hg19">Human genome (hg19)</option>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
102 <option value="mm9">Mouse genome (mm9)</option>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
103 <option value="mm10">Mouse genome (mm10)</option>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
104 </param>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
105 <param argument="-hm" name="homopolymer_size" type="integer" value="3" min="2"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
106 label="Homopolymer size"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
107 help="Affected plot: Homopolymer indels; sets the minimal number of consecutive bases that define a homopolymer" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
108 </section>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
109 </inputs>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
110 <outputs>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
111 <data name="output_html" format="html"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
112 label="${tool.name} report on ${on_string}" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
113 <data name="output_per_base_coverage" format="tsv"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
114 label="${tool.name} per-base coverage on ${on_string}">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
115 <filter>per_base_coverage</filter>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
116 </data>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
117 <collection name="raw_data" type="list"
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
118 label="Raw data for ${tool.name} on ${on_string}">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
119 <data name="genome_results" format="txt" from_work_dir="results/summary_report.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
120 <data name="coverage_across_reference" format="tsv" from_work_dir="results/coverage_across_reference.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
121 <data name="coverage_histogram" format="tsv" from_work_dir="results/coverage_histogram.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
122 <data name="genome_fraction_coverage" format="tsv" from_work_dir="results/genome_fraction_coverage.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
123 <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
124 <data name="mapped_reads_clipping_profile" format="tsv" from_work_dir="results/mapped_reads_clipping_profile.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
125 <data name="mapped_reads_gc-content_distribution" format="tsv" from_work_dir="results/mapped_reads_gc-content_distribution.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
126 <data name="mapped_reads_nucleotide_content" format="tsv" from_work_dir="results/mapped_reads_nucleotide_content.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
127 <data name="mapping_quality_across_reference" format="tsv" from_work_dir="results/mapping_quality_across_reference.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
128 <data name="mapping_quality_histogram" format="tsv" from_work_dir="results/mapping_quality_histogram.txt" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
129 </collection>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
130 </outputs>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
131 <tests>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
132 <test expect_num_outputs="12">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
133 <param name="input1" value="test_mapped_reads.bam"/>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
134 <output name="output_html" ftype="html">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
135 <assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
136 <has_text text="Qualimap report: BAM QC" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
137 </assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
138 </output>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
139 <output_collection name="raw_data" type="list">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
140 <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
141 </output_collection>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
142 </test>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
143 <test expect_num_outputs="13">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
144 <param name="input1" value="test_mapped_reads.bam" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
145 <param name="per_base_coverage" value="true" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
146 <output name="output_html" ftype="html">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
147 <assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
148 <has_text text="Qualimap report: BAM QC" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
149 </assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
150 </output>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
151 <output name="output_per_base_coverage" file="per_base_coverage_default.txt" ftype="tsv" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
152 <output_collection name="raw_data" type="list">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
153 <element name="genome_results" file="genome_results_default.txt" ftype="txt" compare="diff" lines_diff="2" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
154 </output_collection>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
155 </test>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
156 <test expect_num_outputs="12">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
157 <param name="input1" value="test_mapped_reads.bam"/>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
158 <conditional name="stats_regions">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
159 <param name="region_select" value="custom_regions" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
160 <param name="regions" value="features.gtf" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
161 </conditional>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
162 <output name="output_html" ftype="html">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
163 <assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
164 <has_text text="Qualimap report: BAM QC" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
165 </assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
166 </output>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
167 <output_collection name="raw_data" type="list">
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
168 <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
169 </output_collection>
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170 </test>
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171 <test expect_num_outputs="13">
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172 <param name="input1" value="test_mapped_reads.bam" />
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173 <conditional name="stats_regions">
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174 <param name="region_select" value="custom_regions" />
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175 <param name="regions" value="features.gtf" />
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176 </conditional>
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177 <param name="per_base_coverage" value="true" />
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178 <output name="output_html" ftype="html">
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179 <assert_contents>
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180 <has_text text="Qualimap report: BAM QC" />
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181 </assert_contents>
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182 </output>
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183 <output name="output_per_base_coverage" file="per_base_coverage_inside_features.txt" ftype="tsv" />
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184 <output_collection name="raw_data" type="list">
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185 <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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186 </output_collection>
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187 </test>
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188 <test expect_num_outputs="13">
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189 <param name="input1" value="test_mapped_reads.bam" />
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190 <conditional name="stats_regions">
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191 <param name="region_select" value="custom_regions" />
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192 <param name="regions" value="features.gtf" />
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193 <param name="outside_stats" value="true" />
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194 </conditional>
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195 <param name="per_base_coverage" value="true" />
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196 <output name="output_html" ftype="html">
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197 <assert_contents>
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198 <has_text text="Qualimap report: BAM QC" />
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199 </assert_contents>
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200 </output>
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201 <output name="output_per_base_coverage" file="per_base_coverage_outside_features.txt" ftype="tsv" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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202 <output_collection name="raw_data" type="list">
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203 <element name="genome_results" file="genome_results_outside_features.txt" ftype="txt" compare="diff" lines_diff="2" />
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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204 </output_collection>
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205 </test>
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206 </tests>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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207 <help><![CDATA[
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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208 **What it does**
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209
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210 **Qualimap BAM QC** lets you evaluate the quality of aligned reads data in BAM
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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211 format. The tool summarizes basic statistics of the alignment (number of reads,
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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212 coverage, GC-content, etc.) and produces a number of useful graphs for their
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213 interpretation.
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214
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215 The analysis can be performed with any kind of sequencing data, such as
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216 whole-genome sequencing, exome sequencing, RNA-seq or ChIP-seq data.
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217
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218 In addition, it is possible to provide an annotation file so the results are
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219 computed for the reads mapping inside (and optionally outside) of the
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220 corresponding genomic regions, which can be especially useful for evaluating
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221 target-enrichment sequencing studies.
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222
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223 Input
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224 =====
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225
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226 *Mapped reads input dataset*
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227
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228 The dataset holding the mapped reads to carry out the analysis with.
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229
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230 *Dataset specifying regions*
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231
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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232 If you decide to calculate mapping statistics for selected regions of the
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233 reference genome (instead of for the whole genome), you need to specify the
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234 regions through this additional dataset in gtf, gff or bed format.
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235
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236 .. class:: infomark
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237
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238 A typical problem when working with regions (and genome annotation data, in general) is potential inconsistency between the chromosome names used in the mapped reads input versus those used to define the regions. In the case of the human genome, for example, UCSC data has chromosomes starting with a 'chr' prefix, which is lacking from Ensemble data. This simple form of the problem is handled by Qualimap: if chromosome names in the regions input have a 'chr' prefix, Qualimap will add that prefix to the mapped reads chromosome names as needed. For more complex cases you will have to adjust your inputs manually.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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239
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240
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241 Parameters
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242 ----------
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243
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244 *Reference genome regions to calculate mapping statistics for*
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245
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246 Choose whether you would like to have mapping statistics reported across
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247
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248 - the entire reference genome
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249 (as specified in the header of the mapped reads input)
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250
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
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251 - specific regions of the reference
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252
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253 In the second case, you need to select a *Dataset specifying regions* (see
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254 above). Using the *Invert regions* switch you can then indicate whether you
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255 want to select or exclude the regions in this dataset.
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256
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257 *Generate per-base coverage output*
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258
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259 *Skip duplicate reads*
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260
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261 The tool lets you skip alignments of duplicate reads from the analysis.
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262 Depending on whether you select none, either one, or both of the available
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263 options, you can decide to:
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264
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265 - not correct for duplicate reads at all (*e.g.* because you have removed them
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266 at an earlier step with some dedicated tool)
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267 - identify and flag duplicate reads with a dedicated tool (like ``Picard
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268 MarkDuplicates`` or ``samtools markdup``), then have Qualimap ignore the
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269 duplicate-flagged reads (recommended, most flexible option since other tools
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270 can be told to ignore the same reads)
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271 - have Qualimap identify potential duplicates by itself and ignore them
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272 - combine external and Qualimap-internal duplicate detection for extra
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273 stringency
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274
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275 Independent of your selection, the HTML report will always list (in the
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276 `Globals` section of the `Summary`) the number of duplicated reads estimated by
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277 Qualimap. If you choose to skip duplicates, you will also be informed about the
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278 number of skipped reads in that same section and, if you instruct Qualimap to
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279 look for the duplicate flag on reads, the number of reads flagged as duplicates
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280 will also be reported here.
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281
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282 **Section: Settings affecting specific plots**
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283
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284 Parameters in this section only affect some (or even only one) of the plots
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285 contained in the HTML report (and the corresponding part of the *Raw Data*
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286 output collection).
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287
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288 For most of these options, the parameter help above should be descriptive
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289 enough. Just a few more words on two of them:
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290
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291 *Number of bins to use in across-reference plots*
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292
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293 This value is used for computing the various graphs that plot information
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294 across the reference. Basically, the reference genome gets split into the given
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295 number of bins, and reads falling in the same bin are aggregated in the
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296 statistics of that bin.
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297
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298 Thus, the higher the number of bins, the higher the resolution of the plots,
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299 but more bins also require longer time for their statistics to be computed.
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300 Less bins, on the other hand, mean more reads will have to be aggregated per
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301 bin and this comes with higher memory requirements. Hence, if the tool fails
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302 with an ``Out Of Memory`` error, you may want to rerun it with a higher bin
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303 number.
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304
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305 *Plot expected GC-content distribution of the following reference genome*
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306
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307 The choice of reference genomes with pre-calculated GC distributions is built
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308 into Qualimap.
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309
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310 Future releases of Qualimap may include more choices, but the current version
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311 is limited to those offered here.
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312
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313
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314 Outputs
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315 =======
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316
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317 HTML Report
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318 -----------
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319
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320 **Summary Section**
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321
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322 *Globals*
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323
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324 This section contains information about the total number of reads, number of mapped reads, paired-end mapping performance, read length distribution,
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325 number of clipped reads and duplication rate (estimated from the start positions of read alignments).
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326
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327 *ACGT Content*
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328
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329 Nucleotide content and GC percentage in the mapped reads.
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330
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331 *Coverage*
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332
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333 Mean and standard deviation of the coverage depth.
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334
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335 *Mapping quality*
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336
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337 Mean mapping quality of the mapped reads.
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338
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339 *Insert size*
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340
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341 Mean, standard deviation and percentiles of the insert size distribution if applicable. The features are computed based on the TLEN field of the SAM file.
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342
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343 *Mismatches and indels*
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344
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345 The section reports general alignment error rate (computed as a ratio of total collected edit distance to the number of mapped bases), total number of mismatches and total number of indels (computed from the CIGAR values). Additionally fraction of the homopolymer indels among total indels is provided. Note, the error rate and mismatches metrics are based on optional fields of a SAM record (NM for edit distance, MD for mismatches). The features are not reported if these fields are missing in the SAM file.
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346
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347 *Chromosome stats*
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348
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349 Number of mapped bases, mean and standard deviation of the coverage depth for each chromosome as defined by the header of the SAM file.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
350
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
351 For region-based analysis the information is given inside of regions, including some additional information like, for example, number of correct strand reads.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
352
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
353
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
354 **Plots**
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
355
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
356 *Coverage Across Reference*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
357
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
358 This plot consists of two figures.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
359 The upper figure provides the coverage distribution (red line) and coverage
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
360 deviation across the reference sequence.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
361 The lower figure shows GC content across reference (black line) together with
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
362 its average value (red dotted line).
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
363
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
364 *Coverage Histogram*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
365
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
366 Histogram of the number of genomic locations having a given coverage rate.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
367 The bins of the x-axis are conveniently scaled by aggregating some coverage
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
368 values in order to produce a representative histogram also in presence of the
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
369 usual NGS peaks of coverage.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
370
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
371 *Coverage Histogram (0-50X)*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
372
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
373 Similar to the previous plot, but in this graph genome locations with a
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
374 coverage greater than 50X are grouped into the last bin.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
375 By doing so a higher resolution of the most common values for the coverage rate
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
376 is obtained.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
377
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
378 *Genome Fraction Coverage*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
379
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
380 Provides a visual way of knowing how much reference has been sequenced to at
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
381 least a given coverage rate.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
382 This graph should be interpreted as in this example:
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
383 If one aims for a coverage rate of at least 25X (x-axis), how much of the
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
384 reference (y-axis) will be considered?
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
385
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
386 *Duplication Rate Histogram*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
387
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
388 This plot shows the distribution of duplicated reads.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
389 Due to several factors (*e.g.* amount of starting material, sample preparation,
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
390 *etc.*) it is possible that the same fragments are sequenced several times.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
391 For some experiments where enrichment is used (*e.g.* ChIP-seq ) this is
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
392 expected to some degree.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
393 For most experiments, however, a high duplication level of the reads indicates
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
394 some unwanted bias.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
395
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
396 *Mapped Reads Nucleotide Content*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
397
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
398 This plot shows the nucleotide content per position of the mapped reads.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
399
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
400 *Mapped Reads GC Content Distribution*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
401
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
402 This graph shows the distribution of GC-content per mapped read.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
403 If compared with a precomputed genome distribution, this plot allows to check
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
404 if there is a shift in the GC content.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
405
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
406 *Mapped Reads Clipping Profile*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
407
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
408 Represents the percentage of clipped bases across the reads.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
409 Technically, the clipping is detected via SAM format CIGAR codes ‘H’
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
410 (hard clipping) and ‘S’ (soft clipping).
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
411 In addition, the total number of clipped reads can be found in the report
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
412 `Summary` section.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
413
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
414 This plot is not shown if no clipped reads are found.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
415
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
416 *Homopolymer Indels*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
417
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
418 This bar plot shows the number of indels that are located within A, C, G and T
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
419 homopolymers, respectively, as well as the number of indels that are not within
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
420 any homopolymer. Large numbers of homopolymer indels may indicate a problem in
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
421 the sequencing process.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
422 Technically, Qualimap identifies indels from the CIGAR code of the aligned
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
423 reads. Indel statistics can also be found in a dedicated section of the report
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
424 `Summary`.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
425
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
426 This graph is not shown if the sample doesn’t contain any indels.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
427
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
428 *Mapping Quality Across Reference*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
429
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
430 This plot provides the mapping quality distribution across the reference.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
431 To construct the plot, the mean mapping quality is computed for each bin.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
432
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
433 *Mapping Quality Histogram*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
434
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
435 Histogram of the number of genomic locations having a given mapping quality.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
436 To construct the histogram the mean mapping quality is computed at each genome
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
437 position with non-zero coverage and collected.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
438 According to the SAM/BAM format specifications, the range for the mapping
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
439 quality score is [0-255].
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
440
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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441 *Insert Size Across Reference*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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442
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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443 This plot provides the insert size distribution across the reference.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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444 Technically, the insert size of each pair of aligned reads is collected from
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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445 the SAM alignment field `TLEN`. Only positive values are taken into account.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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446 To construct the plot, the mean insert size is computed for each bin.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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447
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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448 *Insert Size Histogram*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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449
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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450 Histogram of insert size distribution.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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451
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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452
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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453 Raw Data
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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454 --------
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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455
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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456 This is a *Collection* of 10 individual datasets.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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457
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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458 The *genome_results* dataset provides a plain-text summary of key statistics,
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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459 most of which can also be found in the *Summary* section of the *HTML Report*.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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460
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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461 The remaining 9 datasets hold the tabular raw data underlying the plots of the corresponding names in the *HTML Report*.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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462
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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463
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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464 Per-base coverage
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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465 -----------------
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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466
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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467 Optional. This is a tabular dataset listing the coverage of every base in the
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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468 reference genome unless that coverage is zero. Since its content is
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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469 uncompressed text, this dataset can easily become huge, and it is recommended
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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470 that you generate this dataset only for very small genomes or very limited
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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471 regions of larger genomes.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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472 ]]> </help>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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473 <expand macro="citations"/>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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474 </tool>