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annotate CoverageReport.xml @ 0:49788db492f7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
author iuc
date Wed, 25 Oct 2017 12:37:17 -0400
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49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
iuc
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1 <tool id="CoverageReport2" name="Panel Coverage Report" version="0.0.4">
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
iuc
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2 <description>Provide mapping statistics</description>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
iuc
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3 <requirements>
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iuc
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4 <requirement type="package" version="1.75">perl-number-format</requirement>
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iuc
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5 <requirement type="package" version="3.4.1">R</requirement>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
iuc
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6 <requirement type="package" version="2.17.0">bedtools</requirement>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
iuc
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7 <requirement type="package" version="0.1.18">samtools</requirement>
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iuc
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8 <requirement type="package" version="0.1.6">tectonic</requirement>
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iuc
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9 </requirements>
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iuc
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10 <command detect_errors="exit_code"><![CDATA[
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11 perl '$__tool_directory__/CoverageReport.pl'
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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12 ## input files
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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13 -b '$input1'
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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14 -t '$input2'
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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15
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16 ## output files
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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17 -o '$output1'
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18
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19 ## run parameters
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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20 $perGene
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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21 $PositionLevel
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22 -m $threshold
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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23 -f $frac
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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24 ## sample name
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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25 -n '$input1.name'
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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26 ]]></command>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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27 <inputs>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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28 <param name="input1" type="data" format="bam" label="BAM file" help="BAM file of mapped reads" />
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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29 <param name="input2" type="data" format="bed" label="Target Regions BED" help="BED file containing regions of interest. See below for format" />
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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30 <param name="threshold" type="integer" value="40" label="Minimal Coverage Threshold" help="Default: 40" />
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
iuc
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31 <param name="frac" type="float" value="0.2" label="Fraction of Average Coverage for usage in plot" help="Default: 0.2" />
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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32 <param name="perGene" type="boolean" truevalue="-r" falsevalue="" checked="True" label="Plot exon coverages for all genes in targets"/>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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33 <param name="PositionLevel" type="select" label="Perform Per Exon Analysis" help="Only Failed: Only those exons not reaching global coverage above threshold, or 100%. All Exons: This can take a very long time for large panels! Select all failed to check all exons for local failures." >
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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34 <option value='' selected="true">None</option>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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35 <option value='-s'>Plot Only Globally Failed</option>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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36 <option value='-S'>Plot All Failed Exons</option>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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37 <option value='-A'>Plot All Exons</option>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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38 <option value='-L'>List All Failed Exons</option>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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39 </param>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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40 </inputs>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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41 <outputs>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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42 <data format="pdf" name="output1" label="${tool.name} on ${on_string}: PDF Report"/>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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43 </outputs>
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44 <tests>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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45 <test>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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46 <param name="input1" value="ecoli.bam" />
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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47 <param name="input2" value="ecoli_6.bed" />
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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48 <output name="output1" value="answer.pdf" compare="sim_size"/>
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 **What it does**
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53
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54 This tool creates a coverage report for QC purposes. By default, average coverage statistics are provided, taken from samtools flagstats. If specified, it can also create overviews per gene in the BED file, and sub-exon plots for failed exons.
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55
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56 ------
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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57
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58 **BED format**
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59
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60 The BED file containing targets of interest has very specific format requirements. You **must** use the following format::
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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61
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62 Column 1: Chromosome : Use the same syntax as the references used by Galaxy. Check your sam-headers for the correct format. ('chr1' vs '1')
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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63 Column 2: Start Position
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64 Column 3: End Position
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65 Column 4: Target Name. Use : "GENE-NAME&lt;space&gt;Exon_number" : This is split on the space after 'GeneName' for correct grouping.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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66 Column 5: Score : ignored, use '0'
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67 Column 6: Strand: ignored,'+' or '-'
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68
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69 .. class:: infomark
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70
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71 Note: The exons for the plots will be ordered in the same way as the exons in the BED file.
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72
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73 ------
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74
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75 **Input formats**
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76
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77 BAM file for reads, BED file for targets.
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78
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79 ------
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81 **Outputs**
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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82
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83 The output files are a PDF report.
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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84 The output tables are (tab seperated txt files):
49788db492f7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/coverage_report commit 1b647bb088f62c1369d963f030caecaa9ee003c7
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85
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86 **Targets.Global.Coverage** : Original BED file + following columns::
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87 - Total coverage in target
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88 - Bases in target with coverage
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89 - Length of target
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90 - Percent of target covered
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91
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92 **Targets.Position.Coverage** : Original BED file + following columns::
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93 - Position in target region
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94 - Coverage at position
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95
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96 ]]></help>
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97 <citations>
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98 <citation type="bibtex">@ARTICLE{a1,
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99 title = {This tool creates a coverage report for QC purposes.},
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100 author = {Philip Mabon},
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101 url = {https://github.com/galaxyproject/tools-iuc/}
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102 }
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103 }</citation>
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104 </citations>
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105 </tool>