Mercurial > repos > iuc > qualimap_bamqc

annotate qualimap_bamqc.xml @ 5:30a201c9c310 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
author iuc
date Thu, 11 Jul 2024 14:42:43 +0000
parents 19ece8afbaab
children
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5
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
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1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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2 <macros>
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3 <import>qualimap_macros.xml</import>
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4 </macros>
5
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5 <expand macro="bio_tools"/>
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import os
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10 #import re
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11 @SET_JAVA_OPTS@ &&
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12
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13 ## Set some default file names and paths
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14 ## where we expect tool output to end up.
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15 ## Note that most of these need to be overwritten if the user is
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16 ## interested in regions *outside* those defined in a custom regions
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17 ## file.
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18 #set $out_dir = 'results'
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19 #set $report_name = 'qualimapReport'
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20 #set $summary_report = 'genome_results.txt'
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21 #set $coverage_file = os.path.join($out_dir, 'coverage.txt')
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22 ## This is the only file path that qualimap does not calculate
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23 ## from $out_dir.
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24 #set $per_base_coverage_target = $coverage_file
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25
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26 #if str($stats_regions.region_select) == 'custom_regions':
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27 ## Have qualimap detect file format by suffix
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28 ## since its autodetection is unreliable.
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29 #set $regions_file = '.'.join(['regions', str($stats_regions.regions.ext)])
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30 ln -s '${stats_regions.regions}' ${regions_file} &&
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31
0
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32 #if $stats_regions.outside_stats:
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33 #set $report_name = 'qualimapReportOutsideRegions'
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34 #set $summary_report = 'outside_results.txt'
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35 #set $coverage_file = os.path.join(
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36 $out_dir, 'outside_coverage.txt'
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37 )
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38 #if $per_base_coverage:
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39 #set $per_base_coverage_target = '/dev/null'
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40 #end if
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41 #end if
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42 #end if
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43
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44 #set input_name = re.sub('[^\w]', '_', str($input1.element_identifier))
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45 ln -s '$input1' '$input_name' &&
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46
1
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47 qualimap bamqc
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48 -bam '$input_name' -outdir results -outformat html
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49 --collect-overlap-pairs
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50 #if str($stats_regions.region_select) == 'custom_regions':
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51 -gff ${regions_file} ${stats_regions.outside_stats}
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52 #end if
0
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53 #if $per_base_coverage:
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54 $per_base_coverage $per_base_coverage_target
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55 #end if
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56 -nw ${plot_specific.n_bins}
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57 ${plot_specific.paint_chromosome_limits}
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58 #if $plot_specific.genome_gc_distr:
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59 --genome-gc-distr ${plot_specific.genome_gc_distr}
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60 #end if
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61 -hm ${plot_specific.homopolymer_size}
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62
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63 #if $duplicate_skipping:
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64 --skip-duplicated
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65 #if str($duplicate_skipping) == '0,1':
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66 --skip-dup-mode 2
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67 #else:
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68 --skip-dup-mode ${duplicate_skipping}
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69 #end if
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70 #end if
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71 -nt \${GALAXY_SLOTS:-1} &&
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72
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73 #if $per_base_coverage:
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74 mv $coverage_file '$output_per_base_coverage' &&
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75 #end if
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76 @MASSAGE_OUTPUT@
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77 ]]></command>
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78 <inputs>
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79 <param name="input1" argument="-bam" type="data" format="bam" label="Mapped reads input dataset" />
0
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80 <conditional name="stats_regions">
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81 <param name="region_select" type="select" label="Reference genome regions to calculate mapping statistics for">
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82 <option value="all">All (whole genome)</option>
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83 <option value="custom_regions">Select regions</option>
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84 </param>
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85 <when value="all" />
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86 <when value="custom_regions">
5
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
87 <param name="regions" argument="-gff" type="data" format="gff,gtf,bed" label="Dataset specifying regions" />
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
88 <param name="outside_stats" argument="-os" type="boolean" truevalue="--outside-stats" falsevalue="" checked="false" label="Invert regions" help="If selected, report read statistics *outside* the regions in the regions file." />
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
89 </when>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
90 </conditional>
5
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
91 <param name="per_base_coverage" argument="-oc" type="boolean" truevalue="--output-genome-coverage" falsevalue="" checked="false" label="Generate per-base coverage output" 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!" />
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
92 <param name="duplicate_skipping" argument="--skip-dup-mode" type="select" optional="true" label="Skip duplicate reads" display="checkboxes" multiple="true">
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
93 <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
94 <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
95 </param>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
96 <section name="plot_specific" title="Settings affecting specific plots" expanded="false">
5
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
97 <param name="n_bins" argument="-nw" type="integer" value="400" label="Number of bins to use in across-reference plots" 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!" />
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
98 <param name="paint_chromosome_limits" argument="-c" type="boolean" truevalue="--paint-chromosome-limits" falsevalue="" checked="true" label="Draw chromosome limits" help="Affected plots: Coverage, Mapping Quality and Insert Size across reference; in across-reference plots, indicate chromosome boundaries with dotted lines and labels" />
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
99 <param name="genome_gc_distr" argument="-gd" type="select" optional="true" label="Plot expected GC-content distribution of the following reference genome" help="Affected plot: Mapped reads GC-content distribution; include a precalculated GC-content distribution for the selected (Qualimap-supported) reference genome in the plot">
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
100 <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
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diff changeset
101 <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
102 <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
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diff changeset
103 </param>
5
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
104 <param name="homopolymer_size" argument="-hm" type="integer" min="2" value="3" label="Homopolymer size" help="Affected plot: Homopolymer indels; sets the minimal number of consecutive bases that define a homopolymer" />
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
105 </section>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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diff changeset
106 </inputs>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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diff changeset
107 <outputs>
5
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
108 <data name="output_html" format="html" label="${tool.name} report on ${on_string}" />
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
109 <data name="output_per_base_coverage" format="tsv" label="${tool.name} per-base coverage on ${on_string}">
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
110 <filter>per_base_coverage</filter>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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diff changeset
111 </data>
5
30a201c9c310 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 25200b2c00364b3d371c14cb4624b246446e548b
iuc
parents: 4
diff changeset
112 <collection name="raw_data" type="list" label="Raw data for ${tool.name} on ${on_string}">
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
113 <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
114 <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
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diff changeset
115 <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
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diff changeset
116 <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
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diff changeset
117 <data name="duplication_rate_histogram" format="tsv" from_work_dir="results/duplication_rate_histogram.txt" />
4
19ece8afbaab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620"
iuc
parents: 3
diff changeset
118 <data name="homopolymer_indels" format="tsv" from_work_dir="results/homopolymer_indels.txt" />
19ece8afbaab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620"
iuc
parents: 3
diff changeset
119 <data name="insert_size_across_reference" format="tsv" from_work_dir="results/insert_size_across_reference.txt" />
19ece8afbaab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620"
iuc
parents: 3
diff changeset
120 <data name="insert_size_histogram" format="tsv" from_work_dir="results/insert_size_histogram.txt" />
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
121 <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
122 <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
123 <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
124 <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
125 <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
126 </collection>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
127 </outputs>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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diff changeset
128 <tests>
4
19ece8afbaab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620"
iuc
parents: 3
diff changeset
129 <test expect_num_outputs="15">
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
130 <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
131 <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
132 <assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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diff changeset
133 <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
134 </assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
135 </output>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
136 <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
137 <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
138 </output_collection>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
139 </test>
4
19ece8afbaab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620"
iuc
parents: 3
diff changeset
140 <test expect_num_outputs="16">
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
141 <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
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diff changeset
142 <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
143 <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
144 <assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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145 <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
146 </assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
147 </output>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
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diff changeset
148 <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
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diff changeset
149 <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
150 <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
151 </output_collection>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
152 </test>
4
19ece8afbaab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620"
iuc
parents: 3
diff changeset
153 <test expect_num_outputs="15">
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
154 <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
155 <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
156 <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
157 <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
158 </conditional>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
159 <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
160 <assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
161 <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
162 </assert_contents>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
163 </output>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
164 <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:
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165 <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" />
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166 </output_collection>
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167 </test>
4
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168 <test expect_num_outputs="16">
0
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169 <param name="input1" value="test_mapped_reads.bam" />
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170 <conditional name="stats_regions">
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171 <param name="region_select" value="custom_regions" />
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172 <param name="regions" value="features.gtf" />
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173 </conditional>
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174 <param name="per_base_coverage" value="true" />
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175 <output name="output_html" ftype="html">
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176 <assert_contents>
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177 <has_text text="Qualimap report: BAM QC" />
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178 </assert_contents>
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179 </output>
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180 <output name="output_per_base_coverage" file="per_base_coverage_inside_features.txt" ftype="tsv" />
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181 <output_collection name="raw_data" type="list">
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182 <element name="genome_results" file="genome_results_inside_features.txt" ftype="txt" compare="diff" lines_diff="2" />
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183 </output_collection>
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184 </test>
4
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185 <test expect_num_outputs="16">
0
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186 <param name="input1" value="test_mapped_reads.bam" />
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187 <conditional name="stats_regions">
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188 <param name="region_select" value="custom_regions" />
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189 <param name="regions" value="features.gtf" />
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190 <param name="outside_stats" value="true" />
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191 </conditional>
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192 <param name="per_base_coverage" value="true" />
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193 <output name="output_html" ftype="html">
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194 <assert_contents>
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195 <has_text text="Qualimap report: BAM QC" />
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196 </assert_contents>
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197 </output>
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198 <output name="output_per_base_coverage" file="per_base_coverage_outside_features.txt" ftype="tsv" />
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199 <output_collection name="raw_data" type="list">
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200 <element name="genome_results" file="genome_results_outside_features.txt" ftype="txt" compare="diff" lines_diff="2" />
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201 </output_collection>
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202 </test>
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203 </tests>
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204 <help><![CDATA[
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205 **What it does**
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206
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207 **Qualimap BAM QC** lets you evaluate the quality of aligned reads data in BAM
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208 format. The tool summarizes basic statistics of the alignment (number of reads,
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209 coverage, GC-content, etc.) and produces a number of useful graphs for their
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210 interpretation.
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211
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212 The analysis can be performed with any kind of sequencing data, such as
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213 whole-genome sequencing, exome sequencing, RNA-seq or ChIP-seq data.
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214
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215 In addition, it is possible to provide an annotation file so the results are
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216 computed for the reads mapping inside (and optionally outside) of the
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217 corresponding genomic regions, which can be especially useful for evaluating
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218 target-enrichment sequencing studies.
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219
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220 Input
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221 =====
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222
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223 *Mapped reads input dataset*
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224
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225 The dataset holding the mapped reads to carry out the analysis with.
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226
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227 *Dataset specifying regions*
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228
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229 If you decide to calculate mapping statistics for selected regions of the
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230 reference genome (instead of for the whole genome), you need to specify the
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231 regions through this additional dataset in gtf, gff or bed format.
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232
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233 .. class:: infomark
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234
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235 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.
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236
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237
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238 Parameters
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239 ----------
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240
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241 *Reference genome regions to calculate mapping statistics for*
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242
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243 Choose whether you would like to have mapping statistics reported across
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244
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245 - the entire reference genome
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246 (as specified in the header of the mapped reads input)
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247
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248 - specific regions of the reference
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249
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250 In the second case, you need to select a *Dataset specifying regions* (see
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251 above). Using the *Invert regions* switch you can then indicate whether you
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252 want to select or exclude the regions in this dataset.
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253
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254 *Generate per-base coverage output*
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255
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256 *Skip duplicate reads*
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257
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258 The tool lets you skip alignments of duplicate reads from the analysis.
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259 Depending on whether you select none, either one, or both of the available
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260 options, you can decide to:
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261
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262 - not correct for duplicate reads at all (*e.g.* because you have removed them
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263 at an earlier step with some dedicated tool)
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264 - identify and flag duplicate reads with a dedicated tool (like ``Picard
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265 MarkDuplicates`` or ``samtools markdup``), then have Qualimap ignore the
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266 duplicate-flagged reads (recommended, most flexible option since other tools
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267 can be told to ignore the same reads)
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268 - have Qualimap identify potential duplicates by itself and ignore them
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269 - combine external and Qualimap-internal duplicate detection for extra
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270 stringency
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271
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272 Independent of your selection, the HTML report will always list (in the
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273 `Globals` section of the `Summary`) the number of duplicated reads estimated by
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274 Qualimap. If you choose to skip duplicates, you will also be informed about the
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275 number of skipped reads in that same section and, if you instruct Qualimap to
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276 look for the duplicate flag on reads, the number of reads flagged as duplicates
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277 will also be reported here.
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278
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279 **Section: Settings affecting specific plots**
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280
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281 Parameters in this section only affect some (or even only one) of the plots
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282 contained in the HTML report (and the corresponding part of the *Raw Data*
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283 output collection).
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284
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285 For most of these options, the parameter help above should be descriptive
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286 enough. Just a few more words on two of them:
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287
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288 *Number of bins to use in across-reference plots*
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289
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290 This value is used for computing the various graphs that plot information
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291 across the reference. Basically, the reference genome gets split into the given
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292 number of bins, and reads falling in the same bin are aggregated in the
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293 statistics of that bin.
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294
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295 Thus, the higher the number of bins, the higher the resolution of the plots,
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296 but more bins also require longer time for their statistics to be computed.
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297 Less bins, on the other hand, mean more reads will have to be aggregated per
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298 bin and this comes with higher memory requirements. Hence, if the tool fails
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299 with an ``Out Of Memory`` error, you may want to rerun it with a higher bin
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300 number.
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301
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302 *Plot expected GC-content distribution of the following reference genome*
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303
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304 The choice of reference genomes with pre-calculated GC distributions is built
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305 into Qualimap.
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306
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307 Future releases of Qualimap may include more choices, but the current version
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308 is limited to those offered here.
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309
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310
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311 Outputs
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312 =======
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313
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314 HTML Report
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315 -----------
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316
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317 **Summary Section**
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318
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319 *Globals*
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320
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321 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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322 number of clipped reads and duplication rate (estimated from the start positions of read alignments).
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323
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324 *ACGT Content*
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325
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326 Nucleotide content and GC percentage in the mapped reads.
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327
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328 *Coverage*
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329
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330 Mean and standard deviation of the coverage depth.
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331
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332 *Mapping quality*
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333
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334 Mean mapping quality of the mapped reads.
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335
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336 *Insert size*
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337
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338 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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339
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340 *Mismatches and indels*
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341
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342 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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343
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344 *Chromosome stats*
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345
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
346 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
347
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
348 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
349
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 **Plots**
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 *Coverage Across Reference*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
354
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
355 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
356 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
357 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
358 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
359 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
360
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
361 *Coverage Histogram*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
362
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
363 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
364 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
365 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
366 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
367
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
368 *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
369
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
370 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
371 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
372 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
373 is obtained.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
374
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
375 *Genome Fraction Coverage*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
376
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
377 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
378 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
379 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
380 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
381 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
382
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
383 *Duplication Rate Histogram*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
384
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
385 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
386 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
387 *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
388 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
389 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
390 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
391 some unwanted bias.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
392
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
393 *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
394
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
395 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
396
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
397 *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
398
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
399 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
400 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
401 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
402
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
403 *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
404
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
405 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
406 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
407 (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
408 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
409 `Summary` section.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
410
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
411 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
412
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
413 *Homopolymer Indels*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
414
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
415 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
416 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
417 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
418 the sequencing process.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
419 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
420 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
421 `Summary`.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
422
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
423 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
424
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
425 *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
426
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
427 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
428 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
429
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
430 *Mapping Quality Histogram*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
431
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
432 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
433 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
434 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
435 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
436 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
437
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
438 *Insert Size Across Reference*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
439
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
440 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
parents:
diff changeset
441 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
parents:
diff changeset
442 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
parents:
diff changeset
443 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
parents:
diff changeset
444
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
445 *Insert Size Histogram*
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
446
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
447 Histogram of insert size distribution.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
448
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
449
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
450 Raw Data
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
451 --------
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
452
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
453 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
parents:
diff changeset
454
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
455 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
parents:
diff changeset
456 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
parents:
diff changeset
457
4
19ece8afbaab "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit e5a96dae9473c2083a2312d1d00b1e55c27e1620"
iuc
parents: 3
diff changeset
458 The remaining 12 datasets hold the tabular raw data underlying the plots of the corresponding names in the *HTML Report*.
0
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
459
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
460
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
461 Per-base coverage
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
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462 -----------------
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
463
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
464 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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465 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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466 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
parents:
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467 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
parents:
diff changeset
468 regions of larger genomes.
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
469 ]]> </help>
ac607906f10a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit b4d43001cc0caa14d760c347fa1c416929f769b2"
iuc
parents:
diff changeset
470 <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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471 </tool>